Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xad Working: n-1-19.cluster.ucsf.bkslab.org:/scratch/xiaobo/216447/xad-8058088.4 Result: /scratch/xiaobo/216447/xad-8058088.4 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xad Task: /mnt/nfs/soft/dock/versions/dock37/DOCK-3.7.4rc1/ligand/generate/build_database_ligand.sh --no-db --no-solv --no-mol2 --single --covalent --pre-tautomerized --permissive-taut-prot /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xad mkdir: created directory `/scratch/xiaobo/216447' mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4' /scratch/xiaobo/216447/xad-8058088.4 /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs NOTICE: Using permissive tautomer and protomer thresholds. Could produce many protomers! STORE_PROTOMERS is not set! Will keep all results to finished directory mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working' mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/protonate' Storing results in /scratch/xiaobo/216447/xad-8058088.4/finished Working in /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 /scratch/xiaobo/216447/xad-8058088.4/working/protonate /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Using inputs as protomers/tautomers. No processing done 443 substances and 1000 protomers extracted Coalesing and merging protomers 1000 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1000 protomers after new stereo-center expansion /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Bulk generating 3D conformations all protomers in /scratch/xiaobo/216447/xad-8058088.4/working/3D mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/216447/xad-8058088.4/working/protonate/xad-protomers-expanded.ism /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' 1001 3D conformations generated for 1000 compounds Building ZINC000480860303 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building' mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for ZINC000480860303 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/1 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000480860303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860303 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 14, 14, 14, 14, 14, 47, 47, 47, 47, 47, 47, 47, 14, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 14, 14, 14, 14, 47, 47, 47, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/2 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/2' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000480860303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860303 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 47, 16, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 16, 16, 16, 16, 47, 47, 47, 16, 16] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/3 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/3' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860303.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000480860303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860303 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 14, 14, 14, 14, 14, 47, 47, 47, 47, 47, 47, 47, 14, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 14, 14, 14, 14, 47, 47, 47, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000480860303 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/finished' Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 Building ZINC000480860303 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for ZINC000480860303 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 1) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/1: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000480860303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860303 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 14, 14, 14, 14, 14, 47, 47, 47, 47, 47, 47, 47, 14, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 14, 14, 14, 14, 47, 47, 47, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 2) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000480860303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860303 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 47, 16, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 16, 16, 16, 16, 47, 47, 47, 16, 16] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 3) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860303.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000480860303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860303 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 14, 14, 14, 14, 14, 47, 47, 47, 47, 47, 47, 47, 14, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 14, 14, 14, 14, 47, 47, 47, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000480860303 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 Building ZINC000480860303 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for ZINC000480860303 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 1) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/1: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000480860303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860303 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 14, 14, 14, 14, 14, 47, 47, 47, 47, 47, 47, 47, 14, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 14, 14, 14, 14, 47, 47, 47, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 2) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000480860303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860303 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 47, 16, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 16, 16, 16, 16, 47, 47, 47, 16, 16] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 3) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860303.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000480860303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860303 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 14, 14, 14, 14, 14, 47, 47, 47, 47, 47, 47, 47, 14, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 14, 14, 14, 14, 47, 47, 47, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000480860303 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860303 Building ZINC000480860304 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000480860304 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/4 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000480860304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860304 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 43, 43, 43, 43, 43, 43, 43, 14, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 14, 14, 14, 14, 43, 43, 43, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/5 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000480860304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860304 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 42, 42, 42, 42, 42, 42, 42, 15, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 15, 15, 15, 15, 42, 42, 42, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/6 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/6' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860304.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000480860304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860304 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 43, 43, 43, 43, 43, 43, 43, 14, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 14, 14, 14, 14, 43, 43, 43, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/7 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/7' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860304.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000480860304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860304 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 42, 42, 42, 42, 42, 42, 42, 15, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 15, 15, 15, 15, 42, 42, 42, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000480860304 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 Building ZINC000480860304 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000480860304 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 4) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000480860304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860304 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 43, 43, 43, 43, 43, 43, 43, 14, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 14, 14, 14, 14, 43, 43, 43, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 5) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000480860304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860304 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 42, 42, 42, 42, 42, 42, 42, 15, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 15, 15, 15, 15, 42, 42, 42, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 6) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860304.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000480860304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860304 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 43, 43, 43, 43, 43, 43, 43, 14, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 14, 14, 14, 14, 43, 43, 43, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 7) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860304.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000480860304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860304 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 42, 42, 42, 42, 42, 42, 42, 15, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 15, 15, 15, 15, 42, 42, 42, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000480860304 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 Building ZINC000480860304 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000480860304 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 4) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000480860304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860304 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 43, 43, 43, 43, 43, 43, 43, 14, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 14, 14, 14, 14, 43, 43, 43, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 5) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000480860304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860304 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 42, 42, 42, 42, 42, 42, 42, 15, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 15, 15, 15, 15, 42, 42, 42, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 6) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860304.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000480860304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860304 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 43, 43, 43, 43, 43, 43, 43, 14, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 14, 14, 14, 14, 43, 43, 43, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 7) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860304.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000480860304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860304 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 42, 42, 42, 42, 42, 42, 42, 15, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 15, 15, 15, 15, 42, 42, 42, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000480860304 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 Building ZINC000480860304 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000480860304 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 4) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000480860304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860304 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 43, 43, 43, 43, 43, 43, 43, 14, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 14, 14, 14, 14, 43, 43, 43, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 5) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000480860304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860304 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 42, 42, 42, 42, 42, 42, 42, 15, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 15, 15, 15, 15, 42, 42, 42, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 6) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860304.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000480860304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860304 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 43, 43, 43, 43, 43, 43, 43, 14, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 14, 14, 14, 14, 43, 43, 43, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 7) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1) `ZINC000480860304.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000480860304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000480860304 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(Cl)c(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 42, 42, 42, 42, 42, 42, 42, 15, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 15, 15, 15, 15, 42, 42, 42, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000480860304 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000480860304 Building ZINC000555117110 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000555117110 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/8 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(c2nc(CC(F)(F)F)no2)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000555117110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000555117110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000555117110 none O=C(NCc1cccc(c2nc(CC(F)(F)F)no2)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 15, 15, 15, 8, 12, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 27, 27, 27, 34, 34, 34, 34, 27, 27, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 15, 15, 15, 34, 34, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/9 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(c2nc(CC(F)(F)F)no2)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000555117110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000555117110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000555117110 none O=C(NCc1cccc(c2nc(CC(F)(F)F)no2)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 15, 15, 15, 8, 12, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 14, 14, 14, 14, 14, 26, 26, 26, 34, 34, 34, 34, 26, 26, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 14, 14, 14, 34, 34, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000555117110 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110 Building ZINC000555117110 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000555117110 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 8) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(c2nc(CC(F)(F)F)no2)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000555117110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000555117110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000555117110 none O=C(NCc1cccc(c2nc(CC(F)(F)F)no2)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 15, 15, 15, 8, 12, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 27, 27, 27, 34, 34, 34, 34, 27, 27, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 15, 15, 15, 34, 34, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 9) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/9: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(c2nc(CC(F)(F)F)no2)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000555117110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000555117110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000555117110 none O=C(NCc1cccc(c2nc(CC(F)(F)F)no2)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 15, 15, 15, 8, 12, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 14, 14, 14, 14, 14, 26, 26, 26, 34, 34, 34, 34, 26, 26, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 14, 14, 14, 34, 34, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000555117110 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555117110 Building ZINC000481100626 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481100626 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/10 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(c2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1) `ZINC000481100626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481100626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481100626 none Cc1cc(C)n(c2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 26, 18, 26, 26, 18, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 26, 26, 40, 40, 40, 40, 40, 40, 40, 40, 26, 26, 18, 18, 10, 10, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 26, 26] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 167 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/11 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/11' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(c2ccc(CCNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1) `ZINC000481100626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481100626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481100626 none Cc1cc(C)n(c2ccc(CCNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 17, 17, 26, 26, 17, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 26, 26, 40, 40, 40, 40, 40, 40, 40, 40, 26, 26, 17, 17, 10, 10, 2, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 26, 26] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 162 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481100626 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626 Building ZINC000481100626 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481100626 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 10) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/10: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(c2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1) `ZINC000481100626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481100626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481100626 none Cc1cc(C)n(c2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 26, 18, 26, 26, 18, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 26, 26, 40, 40, 40, 40, 40, 40, 40, 40, 26, 26, 18, 18, 10, 10, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 26, 26] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 167 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 11) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(c2ccc(CCNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1) `ZINC000481100626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481100626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481100626 none Cc1cc(C)n(c2ccc(CCNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 17, 17, 26, 26, 17, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 26, 26, 40, 40, 40, 40, 40, 40, 40, 40, 26, 26, 17, 17, 10, 10, 2, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 26, 26] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 162 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481100626 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481100626 Building ZINC000481189805 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481189805 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/12 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2cc(Br)c(Cl)cc21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481189805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481189805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000481189805 none O=C(N1CCOc2cc(Br)c(Cl)cc21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 17, 1, 16, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 10, 10, 10, 10, 18, 18, 12, 18, 18, 10, 17, 17, 17, 17, 17, 17, 10, 18, 18, 18, 18, 18, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/13 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2cc(Br)c(Cl)cc21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481189805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481189805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000481189805 none O=C(N1CCOc2cc(Br)c(Cl)cc21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 17, 1, 16, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 10, 10, 10, 10, 18, 18, 10, 18, 18, 10, 17, 17, 17, 17, 17, 17, 10, 18, 18, 12, 18, 18, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481189805 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805 Building ZINC000481189805 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481189805 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 12) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2cc(Br)c(Cl)cc21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481189805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481189805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000481189805 none O=C(N1CCOc2cc(Br)c(Cl)cc21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 17, 1, 16, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 10, 10, 10, 10, 18, 18, 12, 18, 18, 10, 17, 17, 17, 17, 17, 17, 10, 18, 18, 18, 18, 18, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 13) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/13: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2cc(Br)c(Cl)cc21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481189805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481189805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000481189805 none O=C(N1CCOc2cc(Br)c(Cl)cc21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 17, 1, 16, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 10, 10, 10, 10, 18, 18, 10, 18, 18, 10, 17, 17, 17, 17, 17, 17, 10, 18, 18, 12, 18, 18, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481189805 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481189805 Building ZINC000481369704 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481369704 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/14 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN(Cc1cccc(Br)c1)C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000481369704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481369704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000481369704 none COC(=O)CCN(Cc1cccc(Br)c1)C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 8, 25, 7, 3, 2, 3, 6, 15, 15, 13, 15, 15, 15, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 8, 8, 7, 7, 6, 6, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/15 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/15' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN(Cc1cccc(Br)c1)C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000481369704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481369704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000481369704 none COC(=O)CCN(Cc1cccc(Br)c1)C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 8, 25, 6, 2, 1, 2, 5, 15, 15, 13, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 8, 8, 6, 6, 5, 5, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [6, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481369704 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704 Building ZINC000481369704 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481369704 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 14) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN(Cc1cccc(Br)c1)C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000481369704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481369704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000481369704 none COC(=O)CCN(Cc1cccc(Br)c1)C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 8, 25, 7, 3, 2, 3, 6, 15, 15, 13, 15, 15, 15, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 8, 8, 7, 7, 6, 6, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 15) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN(Cc1cccc(Br)c1)C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000481369704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481369704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000481369704 none COC(=O)CCN(Cc1cccc(Br)c1)C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 8, 25, 6, 2, 1, 2, 5, 15, 15, 13, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 8, 8, 6, 6, 5, 5, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [6, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481369704 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481369704 Building ZINC000481392377 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481392377 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/16 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN(Cc1cccc(Br)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000481392377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481392377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000481392377 none COC(=O)CCN(Cc1cccc(Br)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 7, 22, 6, 2, 1, 2, 5, 12, 12, 10, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 7, 7, 6, 6, 5, 5, 12, 12, 12, 12, 1, 1, 1, 1] 50 rigid atoms, others: [6, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/17 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/17' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN(Cc1cccc(Br)c1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000481392377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481392377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000481392377 none COC(=O)CCN(Cc1cccc(Br)c1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 7, 22, 6, 2, 1, 2, 5, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 7, 7, 6, 6, 5, 5, 12, 12, 12, 12, 1, 1, 1, 1] 50 rigid atoms, others: [6, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481392377 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377 Building ZINC000481392377 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481392377 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 16) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN(Cc1cccc(Br)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000481392377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481392377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000481392377 none COC(=O)CCN(Cc1cccc(Br)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 7, 22, 6, 2, 1, 2, 5, 12, 12, 10, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 7, 7, 6, 6, 5, 5, 12, 12, 12, 12, 1, 1, 1, 1] 50 rigid atoms, others: [6, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 17) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN(Cc1cccc(Br)c1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000481392377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481392377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000481392377 none COC(=O)CCN(Cc1cccc(Br)c1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 7, 22, 6, 2, 1, 2, 5, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 7, 7, 6, 6, 5, 5, 12, 12, 12, 12, 1, 1, 1, 1] 50 rigid atoms, others: [6, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481392377 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481392377 Building ZINC000555682364 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000555682364 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/18 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCNc1ccc(S(=O)(=O)N(C)C)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000555682364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000555682364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000555682364 none CCCCNc1ccc(S(=O)(=O)N(C)C)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 19, 14, 8, 8, 8, 5, 8, 8, 18, 18, 18, 20, 20, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 35, 35, 35, 35, 35, 35, 19, 19, 14, 8, 8, 20, 20, 20, 20, 20, 20, 8, 3, 3, 3, 3, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/19 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCNc1ccc(S(=O)(=O)N(C)C)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000555682364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000555682364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000555682364 none CCCCNc1ccc(S(=O)(=O)N(C)C)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 34, 17, 13, 8, 8, 8, 5, 8, 8, 18, 18, 18, 19, 19, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 35, 35, 35, 35, 34, 34, 17, 17, 13, 8, 8, 19, 19, 19, 19, 19, 19, 8, 3, 3, 3, 3, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000555682364 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364 Building ZINC000555682364 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000555682364 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 18) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCNc1ccc(S(=O)(=O)N(C)C)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000555682364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000555682364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000555682364 none CCCCNc1ccc(S(=O)(=O)N(C)C)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 19, 14, 8, 8, 8, 5, 8, 8, 18, 18, 18, 20, 20, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 35, 35, 35, 35, 35, 35, 19, 19, 14, 8, 8, 20, 20, 20, 20, 20, 20, 8, 3, 3, 3, 3, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 19) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCNc1ccc(S(=O)(=O)N(C)C)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000555682364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000555682364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000555682364 none CCCCNc1ccc(S(=O)(=O)N(C)C)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 34, 17, 13, 8, 8, 8, 5, 8, 8, 18, 18, 18, 19, 19, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 35, 35, 35, 35, 34, 34, 17, 17, 13, 8, 8, 19, 19, 19, 19, 19, 19, 8, 3, 3, 3, 3, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000555682364 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000555682364 Building ZINC000481623412 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481623412 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/20 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(Cl)c1F) `ZINC000481623412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481623412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000481623412 none COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(Cl)c1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 10, 32, 10, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 10, 10, 10, 10, 10, 32, 32, 32, 10, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/21 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(Cl)c1F) `ZINC000481623412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481623412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000481623412 none COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(Cl)c1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 10, 30, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 10, 10, 10, 10, 10, 30, 30, 30, 10, 2, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481623412 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412 Building ZINC000481623412 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481623412 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 20) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(Cl)c1F) `ZINC000481623412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481623412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000481623412 none COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(Cl)c1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 10, 32, 10, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 10, 10, 10, 10, 10, 32, 32, 32, 10, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 21) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/21: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(Cl)c1F) `ZINC000481623412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481623412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000481623412 none COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(Cl)c1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 10, 30, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 10, 10, 10, 10, 10, 30, 30, 30, 10, 2, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481623412 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481623412 Building ZINC000481666478 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000481666478 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/22 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@](C(C)C)CC2)c1) `ZINC000481666478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481666478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000481666478 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@](C(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 19, 43, 43, 43, 43, 44, 44, 43, 43, 8, 8, 8, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 8, 43, 43, 43, 43, 44, 44, 44, 44, 44, 44, 44, 43, 43, 43, 43, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 80 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/23 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@@](C(C)C)CC2)c1) `ZINC000481666478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481666478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000481666478 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@@](C(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 19, 41, 41, 41, 41, 42, 42, 41, 41, 8, 8, 8, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 8, 41, 41, 41, 41, 42, 42, 42, 42, 42, 42, 42, 41, 41, 41, 41, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 78 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/24 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/24' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@](C(C)C)CC2)c1) `ZINC000481666478.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000481666478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000481666478 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@](C(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 19, 40, 40, 40, 40, 43, 43, 40, 40, 8, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 8, 40, 40, 40, 40, 43, 43, 43, 43, 43, 43, 43, 40, 40, 40, 40, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 91 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/25 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/25' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@@](C(C)C)CC2)c1) `ZINC000481666478.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000481666478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000481666478 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@@](C(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 19, 41, 41, 41, 41, 45, 45, 41, 41, 8, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 8, 41, 41, 41, 41, 45, 45, 45, 45, 45, 45, 45, 41, 41, 41, 41, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 97 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481666478 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 Building ZINC000481666478 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000481666478 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 22) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@](C(C)C)CC2)c1) `ZINC000481666478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481666478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000481666478 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@](C(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 19, 43, 43, 43, 43, 44, 44, 43, 43, 8, 8, 8, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 8, 43, 43, 43, 43, 44, 44, 44, 44, 44, 44, 44, 43, 43, 43, 43, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 80 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 23) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@@](C(C)C)CC2)c1) `ZINC000481666478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481666478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000481666478 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@@](C(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 19, 41, 41, 41, 41, 42, 42, 41, 41, 8, 8, 8, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 8, 41, 41, 41, 41, 42, 42, 42, 42, 42, 42, 42, 41, 41, 41, 41, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 78 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 24) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@](C(C)C)CC2)c1) `ZINC000481666478.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000481666478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000481666478 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@](C(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 19, 40, 40, 40, 40, 43, 43, 40, 40, 8, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 8, 40, 40, 40, 40, 43, 43, 43, 43, 43, 43, 43, 40, 40, 40, 40, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 91 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 25) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@@](C(C)C)CC2)c1) `ZINC000481666478.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000481666478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000481666478 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@@](C(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 19, 41, 41, 41, 41, 45, 45, 41, 41, 8, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 8, 41, 41, 41, 41, 45, 45, 45, 45, 45, 45, 45, 41, 41, 41, 41, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 97 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481666478 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 Building ZINC000481666478 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000481666478 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 22) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@](C(C)C)CC2)c1) `ZINC000481666478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481666478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000481666478 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@](C(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 19, 43, 43, 43, 43, 44, 44, 43, 43, 8, 8, 8, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 8, 43, 43, 43, 43, 44, 44, 44, 44, 44, 44, 44, 43, 43, 43, 43, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 80 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 23) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@@](C(C)C)CC2)c1) `ZINC000481666478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481666478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000481666478 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@@](C(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 19, 41, 41, 41, 41, 42, 42, 41, 41, 8, 8, 8, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 8, 41, 41, 41, 41, 42, 42, 42, 42, 42, 42, 42, 41, 41, 41, 41, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 78 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 24) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@](C(C)C)CC2)c1) `ZINC000481666478.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000481666478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000481666478 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@](C(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 19, 40, 40, 40, 40, 43, 43, 40, 40, 8, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 8, 40, 40, 40, 40, 43, 43, 43, 43, 43, 43, 43, 40, 40, 40, 40, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 91 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 25) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@@](C(C)C)CC2)c1) `ZINC000481666478.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000481666478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000481666478 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@@](C(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 19, 41, 41, 41, 41, 45, 45, 41, 41, 8, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 8, 41, 41, 41, 41, 45, 45, 45, 45, 45, 45, 45, 41, 41, 41, 41, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 97 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481666478 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 Building ZINC000481666478 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000481666478 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 22) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@](C(C)C)CC2)c1) `ZINC000481666478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481666478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000481666478 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@](C(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 19, 43, 43, 43, 43, 44, 44, 43, 43, 8, 8, 8, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 8, 43, 43, 43, 43, 44, 44, 44, 44, 44, 44, 44, 43, 43, 43, 43, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 80 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 23) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@@](C(C)C)CC2)c1) `ZINC000481666478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481666478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000481666478 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@@](C(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 19, 41, 41, 41, 41, 42, 42, 41, 41, 8, 8, 8, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 8, 41, 41, 41, 41, 42, 42, 42, 42, 42, 42, 42, 41, 41, 41, 41, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 78 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 24) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@](C(C)C)CC2)c1) `ZINC000481666478.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000481666478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000481666478 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@](C(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 19, 40, 40, 40, 40, 43, 43, 40, 40, 8, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 8, 40, 40, 40, 40, 43, 43, 43, 43, 43, 43, 43, 40, 40, 40, 40, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 91 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 25) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@@](C(C)C)CC2)c1) `ZINC000481666478.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000481666478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000481666478 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc([N@]2CC[N@@](C(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 19, 41, 41, 41, 41, 45, 45, 41, 41, 8, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 8, 41, 41, 41, 41, 45, 45, 45, 45, 45, 45, 45, 41, 41, 41, 41, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 97 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481666478 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481666478 Building ZINC000600460997 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000600460997 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/26 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccccc2F)C1) `ZINC000600460997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000600460997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000600460997 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccccc2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 31, 31, 16, 31, 31, 31, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 16, 16, 31, 31, 31, 31, 3, 3] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/27 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccccc2F)C1) `ZINC000600460997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000600460997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000600460997 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccccc2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 31, 31, 17, 31, 31, 31, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 17, 17, 31, 31, 31, 31, 3, 3] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000600460997 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997 Building ZINC000600460997 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000600460997 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 26) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccccc2F)C1) `ZINC000600460997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000600460997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000600460997 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccccc2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 31, 31, 16, 31, 31, 31, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 16, 16, 31, 31, 31, 31, 3, 3] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 27) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccccc2F)C1) `ZINC000600460997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000600460997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000600460997 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccccc2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 31, 31, 17, 31, 31, 31, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 17, 17, 31, 31, 31, 31, 3, 3] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000600460997 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000600460997 Building ZINC000481685420 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481685420 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/28 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCOc1ccc(C(F)(F)F)cn1) `ZINC000481685420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481685420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000481685420 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCOc1ccc(C(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 16, 30, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 11, 11, 16, 16, 30, 30, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/29 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCOc1ccc(C(F)(F)F)cn1) `ZINC000481685420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481685420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000481685420 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCOc1ccc(C(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 17, 31, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 11, 11, 17, 17, 31, 31, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481685420 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420 Building ZINC000481685420 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481685420 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 28) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/28: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCOc1ccc(C(F)(F)F)cn1) `ZINC000481685420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481685420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000481685420 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCOc1ccc(C(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 16, 30, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 11, 11, 16, 16, 30, 30, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 29) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/29: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCOc1ccc(C(F)(F)F)cn1) `ZINC000481685420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481685420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000481685420 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCOc1ccc(C(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 17, 31, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 11, 11, 17, 17, 31, 31, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481685420 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481685420 Building ZINC000481758391 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481758391 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/30 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cn(c2cccc(Br)c2)nn1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000481758391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481758391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000481758391 none CN(Cc1cn(c2cccc(Br)c2)nn1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 17, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 11, 21, 21, 21, 38, 38, 38, 38, 38, 38, 21, 21, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 11, 11, 21, 38, 38, 38, 38, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/31 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cn(c2cccc(Br)c2)nn1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000481758391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481758391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000481758391 none CN(Cc1cn(c2cccc(Br)c2)nn1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 17, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 11, 21, 21, 21, 38, 38, 38, 38, 38, 38, 21, 21, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 11, 11, 21, 38, 38, 38, 38, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481758391 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391 Building ZINC000481758391 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481758391 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 30) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/30: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cn(c2cccc(Br)c2)nn1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000481758391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481758391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000481758391 none CN(Cc1cn(c2cccc(Br)c2)nn1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 17, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 11, 21, 21, 21, 38, 38, 38, 38, 38, 38, 21, 21, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 11, 11, 21, 38, 38, 38, 38, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 31) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/31: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cn(c2cccc(Br)c2)nn1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000481758391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481758391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000481758391 none CN(Cc1cn(c2cccc(Br)c2)nn1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 17, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 11, 21, 21, 21, 38, 38, 38, 38, 38, 38, 21, 21, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 11, 11, 21, 38, 38, 38, 38, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481758391 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481758391 Building ZINC000481867124 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481867124 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/32 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1csc(c2cccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)n1) `ZINC000481867124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481867124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000481867124 none COC(=O)c1csc(c2cccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 18, 27, 27, 27, 27, 27, 18, 18, 18, 5, 5, 1, 2, 2, 4, 4, 4, 2, 18] 50 rigid atoms, others: [39, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/33 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1csc(c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)n1) `ZINC000481867124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481867124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000481867124 none COC(=O)c1csc(c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 18, 27, 27, 27, 27, 27, 18, 18, 18, 5, 5, 1, 2, 2, 4, 4, 4, 2, 18] 50 rigid atoms, others: [39, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481867124 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124 Building ZINC000481867124 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481867124 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 32) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/32: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1csc(c2cccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)n1) `ZINC000481867124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481867124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000481867124 none COC(=O)c1csc(c2cccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 18, 27, 27, 27, 27, 27, 18, 18, 18, 5, 5, 1, 2, 2, 4, 4, 4, 2, 18] 50 rigid atoms, others: [39, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 33) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/33: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1csc(c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)n1) `ZINC000481867124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481867124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000481867124 none COC(=O)c1csc(c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 18, 27, 27, 27, 27, 27, 18, 18, 18, 5, 5, 1, 2, 2, 4, 4, 4, 2, 18] 50 rigid atoms, others: [39, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481867124 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481867124 Building ZINC000481874690 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000481874690 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/34 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481874690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874690 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 22, 31, 31, 22, 31, 31, 15, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 22, 22, 31, 31, 22, 31, 31, 15, 15, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 120 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/35 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/35' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481874690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874690 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 22, 31, 31, 22, 31, 31, 15, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 22, 22, 31, 31, 22, 31, 31, 15, 15, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 120 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/36 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/36' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874690.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000481874690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874690 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 24, 24, 19, 24, 24, 12, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 24, 24, 19, 24, 24, 12, 12, 6, 10, 10, 6, 10, 10, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 100 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/37 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/37' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874690.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000481874690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874690 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 24, 24, 19, 24, 24, 12, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 24, 24, 19, 24, 24, 12, 12, 6, 10, 10, 6, 10, 10, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 100 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481874690 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 Building ZINC000481874690 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000481874690 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 34) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/34: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481874690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874690 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 22, 31, 31, 22, 31, 31, 15, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 22, 22, 31, 31, 22, 31, 31, 15, 15, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 120 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 35) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/35: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481874690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874690 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 22, 31, 31, 22, 31, 31, 15, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 22, 22, 31, 31, 22, 31, 31, 15, 15, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 120 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 36) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874690.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000481874690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874690 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 24, 24, 19, 24, 24, 12, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 24, 24, 19, 24, 24, 12, 12, 6, 10, 10, 6, 10, 10, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 100 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 37) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/37: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874690.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000481874690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874690 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 24, 24, 19, 24, 24, 12, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 24, 24, 19, 24, 24, 12, 12, 6, 10, 10, 6, 10, 10, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 100 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481874690 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 Building ZINC000481874690 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000481874690 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 34) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/34: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481874690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874690 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 22, 31, 31, 22, 31, 31, 15, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 22, 22, 31, 31, 22, 31, 31, 15, 15, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 120 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 35) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/35: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481874690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874690 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 22, 31, 31, 22, 31, 31, 15, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 22, 22, 31, 31, 22, 31, 31, 15, 15, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 120 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 36) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874690.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000481874690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874690 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 24, 24, 19, 24, 24, 12, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 24, 24, 19, 24, 24, 12, 12, 6, 10, 10, 6, 10, 10, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 100 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 37) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/37: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874690.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000481874690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874690 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 24, 24, 19, 24, 24, 12, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 24, 24, 19, 24, 24, 12, 12, 6, 10, 10, 6, 10, 10, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 100 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481874690 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 Building ZINC000481874690 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000481874690 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 34) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/34: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481874690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874690 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 22, 31, 31, 22, 31, 31, 15, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 22, 22, 31, 31, 22, 31, 31, 15, 15, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 120 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 35) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/35: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481874690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874690 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 22, 31, 31, 22, 31, 31, 15, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 22, 22, 31, 31, 22, 31, 31, 15, 15, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 120 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 36) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874690.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000481874690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874690 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 24, 24, 19, 24, 24, 12, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 24, 24, 19, 24, 24, 12, 12, 6, 10, 10, 6, 10, 10, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 100 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 37) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/37: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874690.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000481874690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874690 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 24, 24, 19, 24, 24, 12, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 24, 24, 19, 24, 24, 12, 12, 6, 10, 10, 6, 10, 10, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 100 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481874690 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874690 Building ZINC000481874692 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000481874692 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/38 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481874692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874692 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 27, 27, 21, 27, 27, 10, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 27, 27, 21, 27, 27, 11, 11, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/39 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481874692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874692 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 27, 27, 21, 27, 27, 10, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 27, 27, 21, 27, 27, 11, 11, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/40 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/40' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874692.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000481874692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874692 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 23, 28, 28, 23, 28, 28, 16, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 23, 23, 28, 28, 23, 28, 28, 16, 16, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/41 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/41' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874692.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000481874692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874692 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 23, 28, 28, 23, 28, 28, 16, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 23, 23, 28, 28, 23, 28, 28, 16, 16, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481874692 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 Building ZINC000481874692 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000481874692 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 38) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/38: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481874692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874692 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 27, 27, 21, 27, 27, 10, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 27, 27, 21, 27, 27, 11, 11, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 39) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/39: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481874692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874692 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 27, 27, 21, 27, 27, 10, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 27, 27, 21, 27, 27, 11, 11, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 40) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874692.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000481874692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874692 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 23, 28, 28, 23, 28, 28, 16, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 23, 23, 28, 28, 23, 28, 28, 16, 16, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 41) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874692.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000481874692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874692 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 23, 28, 28, 23, 28, 28, 16, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 23, 23, 28, 28, 23, 28, 28, 16, 16, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481874692 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 Building ZINC000481874692 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000481874692 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 38) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/38: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481874692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874692 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 27, 27, 21, 27, 27, 10, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 27, 27, 21, 27, 27, 11, 11, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 39) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/39: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481874692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874692 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 27, 27, 21, 27, 27, 10, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 27, 27, 21, 27, 27, 11, 11, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 40) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874692.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000481874692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874692 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 23, 28, 28, 23, 28, 28, 16, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 23, 23, 28, 28, 23, 28, 28, 16, 16, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 41) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874692.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000481874692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874692 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 23, 28, 28, 23, 28, 28, 16, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 23, 23, 28, 28, 23, 28, 28, 16, 16, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481874692 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 Building ZINC000481874692 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000481874692 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 38) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/38: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481874692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874692 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 27, 27, 21, 27, 27, 10, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 27, 27, 21, 27, 27, 11, 11, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 39) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/39: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481874692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874692 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 27, 27, 21, 27, 27, 10, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 27, 27, 21, 27, 27, 11, 11, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 40) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874692.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000481874692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874692 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 23, 28, 28, 23, 28, 28, 16, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 23, 23, 28, 28, 23, 28, 28, 16, 16, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 41) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874692.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000481874692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874692 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 23, 28, 28, 23, 28, 28, 16, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 23, 23, 28, 28, 23, 28, 28, 16, 16, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481874692 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874692 Building ZINC000481874694 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000481874694 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/42 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481874694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874694 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 24, 24, 17, 24, 24, 11, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 24, 24, 17, 24, 24, 11, 11, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 114 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/43 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481874694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874694 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 24, 24, 17, 24, 24, 11, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 24, 24, 17, 24, 24, 11, 11, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 114 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/44 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/44' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874694.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000481874694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874694 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 28, 28, 20, 28, 28, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 28, 28, 20, 28, 28, 13, 13, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 109 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/45 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/45' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874694.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000481874694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874694 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 28, 28, 20, 28, 28, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 28, 28, 20, 28, 28, 13, 13, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 109 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481874694 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 Building ZINC000481874694 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000481874694 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 42) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/42: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481874694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874694 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 24, 24, 17, 24, 24, 11, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 24, 24, 17, 24, 24, 11, 11, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 114 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 43) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/43: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481874694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874694 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 24, 24, 17, 24, 24, 11, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 24, 24, 17, 24, 24, 11, 11, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 114 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 44) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874694.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000481874694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874694 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 28, 28, 20, 28, 28, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 28, 28, 20, 28, 28, 13, 13, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 109 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 45) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874694.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000481874694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874694 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 28, 28, 20, 28, 28, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 28, 28, 20, 28, 28, 13, 13, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 109 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481874694 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 Building ZINC000481874694 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000481874694 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 42) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/42: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481874694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874694 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 24, 24, 17, 24, 24, 11, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 24, 24, 17, 24, 24, 11, 11, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 114 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 43) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/43: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481874694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874694 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 24, 24, 17, 24, 24, 11, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 24, 24, 17, 24, 24, 11, 11, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 114 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 44) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874694.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000481874694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874694 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 28, 28, 20, 28, 28, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 28, 28, 20, 28, 28, 13, 13, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 109 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 45) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874694.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000481874694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874694 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 28, 28, 20, 28, 28, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 28, 28, 20, 28, 28, 13, 13, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 109 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481874694 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 Building ZINC000481874694 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000481874694 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 42) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/42: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481874694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874694 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 24, 24, 17, 24, 24, 11, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 24, 24, 17, 24, 24, 11, 11, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 114 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 43) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/43: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481874694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874694 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 24, 24, 17, 24, 24, 11, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 24, 24, 17, 24, 24, 11, 11, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 114 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 44) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874694.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000481874694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874694 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 28, 28, 20, 28, 28, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 28, 28, 20, 28, 28, 13, 13, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 109 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 45) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874694.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000481874694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874694 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 28, 28, 20, 28, 28, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 28, 28, 20, 28, 28, 13, 13, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 109 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481874694 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874694 Building ZINC000481874696 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000481874696 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/46 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481874696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874696 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 27, 27, 21, 27, 27, 13, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 27, 27, 21, 27, 27, 13, 13, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/47 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481874696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874696 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 27, 27, 21, 27, 27, 13, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 27, 27, 21, 27, 27, 13, 13, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/48 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/48' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874696.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000481874696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874696 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 28, 28, 26, 28, 28, 15, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 28, 28, 25, 28, 28, 15, 15, 6, 7, 7, 6, 7, 7, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/49 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/49' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874696.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000481874696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874696 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 28, 28, 26, 28, 28, 15, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 28, 28, 25, 28, 28, 15, 15, 6, 7, 7, 6, 7, 7, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481874696 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 Building ZINC000481874696 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000481874696 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 46) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/46: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481874696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874696 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 27, 27, 21, 27, 27, 13, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 27, 27, 21, 27, 27, 13, 13, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 47) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/47: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481874696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874696 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 27, 27, 21, 27, 27, 13, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 27, 27, 21, 27, 27, 13, 13, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 48) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/48: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874696.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000481874696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874696 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 28, 28, 26, 28, 28, 15, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 28, 28, 25, 28, 28, 15, 15, 6, 7, 7, 6, 7, 7, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 49) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/49: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874696.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000481874696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874696 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 28, 28, 26, 28, 28, 15, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 28, 28, 25, 28, 28, 15, 15, 6, 7, 7, 6, 7, 7, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481874696 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 Building ZINC000481874696 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000481874696 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 46) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/46: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481874696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874696 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 27, 27, 21, 27, 27, 13, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 27, 27, 21, 27, 27, 13, 13, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 47) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/47: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481874696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874696 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 27, 27, 21, 27, 27, 13, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 27, 27, 21, 27, 27, 13, 13, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 48) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/48: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874696.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000481874696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874696 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 28, 28, 26, 28, 28, 15, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 28, 28, 25, 28, 28, 15, 15, 6, 7, 7, 6, 7, 7, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 49) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/49: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874696.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000481874696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874696 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 28, 28, 26, 28, 28, 15, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 28, 28, 25, 28, 28, 15, 15, 6, 7, 7, 6, 7, 7, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481874696 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 Building ZINC000481874696 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000481874696 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 46) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/46: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481874696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874696 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 27, 27, 21, 27, 27, 13, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 27, 27, 21, 27, 27, 13, 13, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 47) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/47: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481874696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874696 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 27, 27, 21, 27, 27, 13, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 27, 27, 21, 27, 27, 13, 13, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 48) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/48: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874696.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000481874696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874696 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 28, 28, 26, 28, 28, 15, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 28, 28, 25, 28, 28, 15, 15, 6, 7, 7, 6, 7, 7, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 49) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/49: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481874696.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000481874696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000481874696 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 28, 28, 26, 28, 28, 15, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 28, 28, 25, 28, 28, 15, 15, 6, 7, 7, 6, 7, 7, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481874696 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481874696 Building ZINC000481890475 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481890475 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/50 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481890475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481890475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000481890475 none C[C@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 15, 25, 25, 25, 25, 25, 25, 25, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 15, 15, 25, 25, 25, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/51 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481890475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481890475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000481890475 none C[C@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 17, 28, 28, 28, 28, 28, 28, 28, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 17, 17, 28, 28, 28, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481890475 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475 Building ZINC000481890475 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481890475 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 50) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/50: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481890475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481890475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000481890475 none C[C@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 15, 25, 25, 25, 25, 25, 25, 25, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 15, 15, 25, 25, 25, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 51) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/51: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481890475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481890475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000481890475 none C[C@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 17, 28, 28, 28, 28, 28, 28, 28, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 17, 17, 28, 28, 28, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481890475 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890475 Building ZINC000481890478 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481890478 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/52 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481890478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481890478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000481890478 none C[C@@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 16, 27, 27, 27, 27, 27, 27, 27, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 27, 27, 27, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/53 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481890478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481890478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000481890478 none C[C@@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 15, 25, 25, 25, 25, 25, 25, 25, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 15, 15, 25, 25, 25, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481890478 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478 Building ZINC000481890478 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481890478 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 52) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/52: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481890478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481890478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000481890478 none C[C@@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 16, 27, 27, 27, 27, 27, 27, 27, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 27, 27, 27, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 53) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/53: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000481890478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481890478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000481890478 none C[C@@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 15, 25, 25, 25, 25, 25, 25, 25, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 15, 15, 25, 25, 25, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000481890478 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000481890478 Building ZINC000615164418 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000615164418 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/54 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1OCC(F)(F)F) `ZINC000615164418.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000615164418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000615164418 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 19, 19, 19, 19, 25, 41, 41, 41, 41, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 11, 11, 19, 19, 19, 19, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/55 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/55' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1OCC(F)(F)F) `ZINC000615164418.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000615164418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000615164418 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 11, 20, 20, 20, 20, 20, 20, 25, 43, 43, 43, 43, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 11, 11, 20, 20, 20, 20, 43, 43] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000615164418 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418 Building ZINC000615164418 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000615164418 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 54) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/54: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1OCC(F)(F)F) `ZINC000615164418.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000615164418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000615164418 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 19, 19, 19, 19, 25, 41, 41, 41, 41, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 11, 11, 19, 19, 19, 19, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 55) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/55: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1OCC(F)(F)F) `ZINC000615164418.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000615164418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000615164418 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 11, 20, 20, 20, 20, 20, 20, 25, 43, 43, 43, 43, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 11, 11, 20, 20, 20, 20, 43, 43] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000615164418 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000615164418 Building ZINC001649005050 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001649005050 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/56 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21)C(F)(F)F) `ZINC001649005050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001649005050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001649005050 none O=C(NCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 17, 13, 4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 17, 17, 13, 13, 4, 4, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/57 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/57' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21)C(F)(F)F) `ZINC001649005050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001649005050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001649005050 none O=C(NCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 17, 11, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 17, 17, 11, 11, 4, 4, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC001649005050 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050 Building ZINC001649005050 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001649005050 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 56) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/56: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21)C(F)(F)F) `ZINC001649005050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001649005050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001649005050 none O=C(NCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 17, 13, 4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 17, 17, 13, 13, 4, 4, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 57) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/57: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21)C(F)(F)F) `ZINC001649005050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001649005050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001649005050 none O=C(NCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 17, 11, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 17, 17, 11, 11, 4, 4, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC001649005050 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005050 Building ZINC001649005049 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001649005049 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/58 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21)C(F)(F)F) `ZINC001649005049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001649005049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001649005049 none O=C(NCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 17, 11, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 17, 17, 11, 11, 5, 5, 3, 3, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/59 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21)C(F)(F)F) `ZINC001649005049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001649005049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001649005049 none O=C(NCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 17, 13, 4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 17, 17, 13, 13, 4, 4, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC001649005049 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049 Building ZINC001649005049 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001649005049 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 58) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/58: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21)C(F)(F)F) `ZINC001649005049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001649005049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001649005049 none O=C(NCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 17, 11, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 17, 17, 11, 11, 5, 5, 3, 3, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 59) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21)C(F)(F)F) `ZINC001649005049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001649005049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001649005049 none O=C(NCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 17, 13, 4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 17, 17, 13, 13, 4, 4, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC001649005049 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649005049 Building ZINC000482354344 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482354344 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/60 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H]2CCC[C@@]2(c2nc(c3ccccc3)no2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000482354344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482354344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000482354344 none O=C(N1C[C@H]2CCC[C@@]2(c2nc(c3ccccc3)no2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 5, 10, 10, 10, 10, 10, 10, 10, 10, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 10, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 37, 37, 37, 37, 37, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/61 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H]2CCC[C@@]2(c2nc(c3ccccc3)no2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000482354344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482354344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000482354344 none O=C(N1C[C@H]2CCC[C@@]2(c2nc(c3ccccc3)no2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 7, 14, 14, 14, 14, 14, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 31, 31, 31, 31, 31, 14, 14, 2, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482354344 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344 Building ZINC000482354344 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482354344 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 60) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/60: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H]2CCC[C@@]2(c2nc(c3ccccc3)no2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000482354344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482354344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000482354344 none O=C(N1C[C@H]2CCC[C@@]2(c2nc(c3ccccc3)no2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 5, 10, 10, 10, 10, 10, 10, 10, 10, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 10, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 37, 37, 37, 37, 37, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 61) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/61: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H]2CCC[C@@]2(c2nc(c3ccccc3)no2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000482354344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482354344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000482354344 none O=C(N1C[C@H]2CCC[C@@]2(c2nc(c3ccccc3)no2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 7, 14, 14, 14, 14, 14, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 31, 31, 31, 31, 31, 14, 14, 2, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482354344 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482354344 Building ZINC000482530945 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482530945 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/62 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC000482530945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482530945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000482530945 none CCN(CC)C(=O)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 28, 25, 28, 31, 13, 25, 2, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 37, 37, 37, 37, 37, 31, 31, 31, 31, 31, 13, 13, 6, 6, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 187 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/63 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC000482530945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482530945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000482530945 none CCN(CC)C(=O)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 26, 23, 26, 29, 14, 23, 4, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 35, 35, 35, 35, 35, 29, 29, 29, 29, 29, 14, 14, 6, 6, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482530945 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945 Building ZINC000482530945 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482530945 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 62) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/62: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC000482530945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482530945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000482530945 none CCN(CC)C(=O)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 28, 25, 28, 31, 13, 25, 2, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 37, 37, 37, 37, 37, 31, 31, 31, 31, 31, 13, 13, 6, 6, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 187 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 63) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/63: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC000482530945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482530945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000482530945 none CCN(CC)C(=O)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 26, 23, 26, 29, 14, 23, 4, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 35, 35, 35, 35, 35, 29, 29, 29, 29, 29, 14, 14, 6, 6, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482530945 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482530945 Building ZINC000482564893 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482564893 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/64 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccc(OCC(F)(F)F)c1) `ZINC000482564893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482564893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000482564893 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccc(OCC(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 28, 28, 28, 28, 28, 47, 49, 49, 49, 49, 28, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 13, 13, 28, 28, 28, 49, 49, 28] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/65 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccc(OCC(F)(F)F)c1) `ZINC000482564893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482564893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000482564893 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccc(OCC(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 26, 26, 26, 26, 26, 47, 50, 50, 50, 50, 26, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 12, 12, 26, 26, 26, 50, 50, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482564893 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893 Building ZINC000482564893 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482564893 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 64) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccc(OCC(F)(F)F)c1) `ZINC000482564893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482564893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000482564893 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccc(OCC(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 28, 28, 28, 28, 28, 47, 49, 49, 49, 49, 28, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 13, 13, 28, 28, 28, 49, 49, 28] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 65) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/65: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccc(OCC(F)(F)F)c1) `ZINC000482564893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482564893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000482564893 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccc(OCC(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 26, 26, 26, 26, 26, 47, 50, 50, 50, 50, 26, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 12, 12, 26, 26, 26, 50, 50, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482564893 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482564893 Building ZINC000482570826 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482570826 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/66 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(OC)c1OC) `ZINC000482570826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482570826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000482570826 none COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 11, 11, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 11, 11, 11, 22, 4, 6, 22, 17, 17, 17, 11, 4, 4, 4, 2, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 11, 22, 22, 22, 23, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 114 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/67 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(OC)c1OC) `ZINC000482570826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482570826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000482570826 none COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 11, 11, 11, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 11, 11, 11, 20, 3, 7, 23, 24, 24, 24, 11, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 11, 20, 20, 20, 24, 23, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 119 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482570826 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826 Building ZINC000482570826 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482570826 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 66) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/66: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(OC)c1OC) `ZINC000482570826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482570826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000482570826 none COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 11, 11, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 11, 11, 11, 22, 4, 6, 22, 17, 17, 17, 11, 4, 4, 4, 2, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 11, 22, 22, 22, 23, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 114 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 67) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/67: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(OC)c1OC) `ZINC000482570826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482570826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000482570826 none COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 11, 11, 11, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 11, 11, 11, 20, 3, 7, 23, 24, 24, 24, 11, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 11, 20, 20, 20, 24, 23, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 119 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482570826 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570826 Building ZINC000482570827 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482570827 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/68 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(OC)c1OC) `ZINC000482570827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482570827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000482570827 none COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 12, 12, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 12, 12, 12, 21, 12, 12, 26, 26, 26, 26, 12, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 12, 21, 21, 21, 26, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 95 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/69 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(OC)c1OC) `ZINC000482570827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482570827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000482570827 none COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 16, 16, 16, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 16, 16, 16, 25, 6, 6, 23, 26, 26, 26, 16, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 16, 25, 25, 25, 23, 23, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 111 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482570827 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827 Building ZINC000482570827 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482570827 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 68) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/68: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(OC)c1OC) `ZINC000482570827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482570827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000482570827 none COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 12, 12, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 12, 12, 12, 21, 12, 12, 26, 26, 26, 26, 12, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 12, 21, 21, 21, 26, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 95 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 69) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/69: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(OC)c1OC) `ZINC000482570827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482570827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000482570827 none COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 16, 16, 16, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 16, 16, 16, 25, 6, 6, 23, 26, 26, 26, 16, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 16, 25, 25, 25, 23, 23, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 111 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482570827 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482570827 Building ZINC000482709360 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482709360 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/70 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(CN(C)C)ccn1) `ZINC000482709360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482709360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000482709360 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(CN(C)C)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 10, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 11, 12, 12, 5, 5, 5, 3, 3, 3, 13, 13, 5, 13, 3, 3, 3, 3, 5, 11, 11, 12, 12, 12, 12, 12, 12, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/71 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(CN(C)C)ccn1) `ZINC000482709360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482709360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000482709360 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(CN(C)C)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 10, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 12, 13, 13, 4, 4, 4, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 4, 12, 12, 13, 13, 13, 13, 13, 13, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482709360 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360 Building ZINC000482709360 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482709360 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 70) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/70: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(CN(C)C)ccn1) `ZINC000482709360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482709360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000482709360 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(CN(C)C)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 10, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 11, 12, 12, 5, 5, 5, 3, 3, 3, 13, 13, 5, 13, 3, 3, 3, 3, 5, 11, 11, 12, 12, 12, 12, 12, 12, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 71) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/71: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(CN(C)C)ccn1) `ZINC000482709360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482709360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000482709360 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(CN(C)C)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 10, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 12, 13, 13, 4, 4, 4, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 4, 12, 12, 13, 13, 13, 13, 13, 13, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482709360 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482709360 Building ZINC000482772896 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482772896 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/72 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(N2CCSCC2)CCCCC1) `ZINC000482772896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482772896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000482772896 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(N2CCSCC2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 14, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 2, 17, 32, 33, 33, 33, 33, 33, 32, 32, 32, 32, 32, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 2, 11, 11, 33, 33, 33, 33, 33, 33, 33, 33, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 122 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/73 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/73' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(N2CCSCC2)CCCCC1) `ZINC000482772896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482772896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000482772896 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(N2CCSCC2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 14, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 2, 18, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 10, 10, 4, 10, 10, 3, 3, 3, 2, 11, 11, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 125 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482772896 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896 Building ZINC000482772896 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482772896 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 72) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/72: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(N2CCSCC2)CCCCC1) `ZINC000482772896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482772896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000482772896 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(N2CCSCC2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 14, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 2, 17, 32, 33, 33, 33, 33, 33, 32, 32, 32, 32, 32, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 2, 11, 11, 33, 33, 33, 33, 33, 33, 33, 33, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 122 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 73) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/73: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(N2CCSCC2)CCCCC1) `ZINC000482772896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482772896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000482772896 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(N2CCSCC2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 14, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 2, 18, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 10, 10, 4, 10, 10, 3, 3, 3, 2, 11, 11, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 125 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482772896 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482772896 Building ZINC000482971321 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482971321 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/74 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1OCCCC(=O)Nc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)cc1) `ZINC000482971321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482971321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000482971321 none Cc1ccccc1OCCCC(=O)Nc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 16, 16, 16, 7, 5, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 16, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [51, 54, 55, 50, 29, 56, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 57, 58]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/75 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1OCCCC(=O)Nc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cccn2C)cc1) `ZINC000482971321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482971321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000482971321 none Cc1ccccc1OCCCC(=O)Nc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cccn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 16, 16, 16, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 16, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [51, 54, 55, 50, 29, 56, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 57, 58]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482971321 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321 Building ZINC000482971321 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482971321 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 74) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/74: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1OCCCC(=O)Nc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)cc1) `ZINC000482971321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482971321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000482971321 none Cc1ccccc1OCCCC(=O)Nc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 16, 16, 16, 7, 5, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 16, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [51, 54, 55, 50, 29, 56, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 57, 58]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 75) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/75: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1OCCCC(=O)Nc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cccn2C)cc1) `ZINC000482971321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482971321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000482971321 none Cc1ccccc1OCCCC(=O)Nc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cccn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 16, 16, 16, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 16, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [51, 54, 55, 50, 29, 56, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 57, 58]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482971321 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482971321 Building ZINC000482967276 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000482967276 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/76 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482967276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967276 none CSc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 17, 17, 24, 24, 17, 11, 17, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 21, 33, 33, 33, 33, 33, 33, 33, 33, 24, 24, 36, 36, 36, 24, 24, 11, 11, 3, 2, 2, 2, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 155 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/77 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482967276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967276 none CSc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 25, 20, 30, 30, 20, 10, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 23, 35, 35, 35, 35, 35, 35, 35, 35, 30, 30, 41, 41, 41, 30, 30, 10, 10, 3, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 35, 35, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 194 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/78 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/78' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967276.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000482967276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967276 none CSc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 17, 17, 24, 24, 17, 11, 17, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 21, 33, 33, 33, 33, 33, 33, 33, 33, 24, 24, 36, 36, 36, 24, 24, 11, 11, 3, 2, 2, 2, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 155 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/79 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/79' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967276.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000482967276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967276 none CSc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 25, 20, 30, 30, 20, 10, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 23, 35, 35, 35, 35, 35, 35, 35, 35, 30, 30, 41, 41, 41, 30, 30, 10, 10, 3, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 35, 35, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 194 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482967276 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 Building ZINC000482967276 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000482967276 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 76) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/76: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482967276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967276 none CSc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 17, 17, 24, 24, 17, 11, 17, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 21, 33, 33, 33, 33, 33, 33, 33, 33, 24, 24, 36, 36, 36, 24, 24, 11, 11, 3, 2, 2, 2, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 155 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 77) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/77: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482967276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967276 none CSc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 25, 20, 30, 30, 20, 10, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 23, 35, 35, 35, 35, 35, 35, 35, 35, 30, 30, 41, 41, 41, 30, 30, 10, 10, 3, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 35, 35, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 194 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 78) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/78: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967276.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000482967276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967276 none CSc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 17, 17, 24, 24, 17, 11, 17, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 21, 33, 33, 33, 33, 33, 33, 33, 33, 24, 24, 36, 36, 36, 24, 24, 11, 11, 3, 2, 2, 2, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 155 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 79) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/79: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967276.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000482967276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967276 none CSc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 25, 20, 30, 30, 20, 10, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 23, 35, 35, 35, 35, 35, 35, 35, 35, 30, 30, 41, 41, 41, 30, 30, 10, 10, 3, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 35, 35, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 194 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482967276 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 Building ZINC000482967276 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000482967276 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 76) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/76: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482967276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967276 none CSc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 17, 17, 24, 24, 17, 11, 17, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 21, 33, 33, 33, 33, 33, 33, 33, 33, 24, 24, 36, 36, 36, 24, 24, 11, 11, 3, 2, 2, 2, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 155 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 77) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/77: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482967276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967276 none CSc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 25, 20, 30, 30, 20, 10, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 23, 35, 35, 35, 35, 35, 35, 35, 35, 30, 30, 41, 41, 41, 30, 30, 10, 10, 3, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 35, 35, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 194 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 78) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/78: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967276.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000482967276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967276 none CSc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 17, 17, 24, 24, 17, 11, 17, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 21, 33, 33, 33, 33, 33, 33, 33, 33, 24, 24, 36, 36, 36, 24, 24, 11, 11, 3, 2, 2, 2, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 155 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 79) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/79: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967276.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000482967276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967276 none CSc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 25, 20, 30, 30, 20, 10, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 23, 35, 35, 35, 35, 35, 35, 35, 35, 30, 30, 41, 41, 41, 30, 30, 10, 10, 3, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 35, 35, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 194 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482967276 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 Building ZINC000482967276 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000482967276 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 76) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/76: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482967276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967276 none CSc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 17, 17, 24, 24, 17, 11, 17, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 21, 33, 33, 33, 33, 33, 33, 33, 33, 24, 24, 36, 36, 36, 24, 24, 11, 11, 3, 2, 2, 2, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 155 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 77) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/77: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482967276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967276 none CSc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 25, 20, 30, 30, 20, 10, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 23, 35, 35, 35, 35, 35, 35, 35, 35, 30, 30, 41, 41, 41, 30, 30, 10, 10, 3, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 35, 35, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 194 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 78) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/78: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967276.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000482967276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967276 none CSc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 17, 17, 24, 24, 17, 11, 17, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 21, 33, 33, 33, 33, 33, 33, 33, 33, 24, 24, 36, 36, 36, 24, 24, 11, 11, 3, 2, 2, 2, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 155 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 79) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/79: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967276.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000482967276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967276 none CSc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 25, 20, 30, 30, 20, 10, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 23, 35, 35, 35, 35, 35, 35, 35, 35, 30, 30, 41, 41, 41, 30, 30, 10, 10, 3, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 35, 35, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 194 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482967276 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967276 Building ZINC000482967277 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000482967277 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/80 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482967277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967277 none CSc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 27, 19, 29, 29, 19, 10, 19, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 20, 35, 35, 35, 35, 35, 35, 35, 35, 29, 29, 39, 39, 39, 29, 29, 10, 10, 3, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 35, 35, 29, 29] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 192 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/81 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/81' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482967277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967277 none CSc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 21, 16, 23, 23, 16, 10, 16, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 20, 33, 33, 33, 33, 33, 33, 33, 33, 23, 23, 35, 35, 35, 23, 23, 10, 10, 3, 2, 2, 2, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 158 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/82 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/82' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967277.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000482967277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967277 none CSc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 27, 19, 29, 29, 19, 10, 19, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 20, 35, 35, 35, 35, 35, 35, 35, 35, 29, 29, 39, 39, 39, 29, 29, 10, 10, 3, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 35, 35, 29, 29] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 192 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/83 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/83' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967277.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000482967277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967277 none CSc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 21, 16, 23, 23, 16, 10, 16, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 20, 33, 33, 33, 33, 33, 33, 33, 33, 23, 23, 35, 35, 35, 23, 23, 10, 10, 3, 2, 2, 2, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 158 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482967277 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 Building ZINC000482967277 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000482967277 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 80) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482967277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967277 none CSc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 27, 19, 29, 29, 19, 10, 19, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 20, 35, 35, 35, 35, 35, 35, 35, 35, 29, 29, 39, 39, 39, 29, 29, 10, 10, 3, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 35, 35, 29, 29] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 192 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 81) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/81: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482967277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967277 none CSc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 21, 16, 23, 23, 16, 10, 16, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 20, 33, 33, 33, 33, 33, 33, 33, 33, 23, 23, 35, 35, 35, 23, 23, 10, 10, 3, 2, 2, 2, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 158 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 82) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/82: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967277.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000482967277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967277 none CSc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 27, 19, 29, 29, 19, 10, 19, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 20, 35, 35, 35, 35, 35, 35, 35, 35, 29, 29, 39, 39, 39, 29, 29, 10, 10, 3, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 35, 35, 29, 29] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 192 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 83) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/83: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967277.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000482967277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967277 none CSc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 21, 16, 23, 23, 16, 10, 16, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 20, 33, 33, 33, 33, 33, 33, 33, 33, 23, 23, 35, 35, 35, 23, 23, 10, 10, 3, 2, 2, 2, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 158 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482967277 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 Building ZINC000482967277 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000482967277 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 80) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482967277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967277 none CSc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 27, 19, 29, 29, 19, 10, 19, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 20, 35, 35, 35, 35, 35, 35, 35, 35, 29, 29, 39, 39, 39, 29, 29, 10, 10, 3, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 35, 35, 29, 29] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 192 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 81) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/81: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482967277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967277 none CSc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 21, 16, 23, 23, 16, 10, 16, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 20, 33, 33, 33, 33, 33, 33, 33, 33, 23, 23, 35, 35, 35, 23, 23, 10, 10, 3, 2, 2, 2, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 158 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 82) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/82: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967277.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000482967277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967277 none CSc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 27, 19, 29, 29, 19, 10, 19, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 20, 35, 35, 35, 35, 35, 35, 35, 35, 29, 29, 39, 39, 39, 29, 29, 10, 10, 3, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 35, 35, 29, 29] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 192 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 83) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/83: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967277.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000482967277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967277 none CSc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 21, 16, 23, 23, 16, 10, 16, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 20, 33, 33, 33, 33, 33, 33, 33, 33, 23, 23, 35, 35, 35, 23, 23, 10, 10, 3, 2, 2, 2, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 158 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482967277 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 Building ZINC000482967277 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000482967277 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 80) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482967277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967277 none CSc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 27, 19, 29, 29, 19, 10, 19, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 20, 35, 35, 35, 35, 35, 35, 35, 35, 29, 29, 39, 39, 39, 29, 29, 10, 10, 3, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 35, 35, 29, 29] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 192 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 81) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/81: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482967277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967277 none CSc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 21, 16, 23, 23, 16, 10, 16, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 20, 33, 33, 33, 33, 33, 33, 33, 33, 23, 23, 35, 35, 35, 23, 23, 10, 10, 3, 2, 2, 2, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 158 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 82) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/82: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967277.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000482967277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967277 none CSc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 27, 19, 29, 29, 19, 10, 19, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 20, 35, 35, 35, 35, 35, 35, 35, 35, 29, 29, 39, 39, 39, 29, 29, 10, 10, 3, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 35, 35, 29, 29] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 192 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 83) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/83: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC000482967277.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000482967277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000482967277 none CSc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 21, 16, 23, 23, 16, 10, 16, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 20, 33, 33, 33, 33, 33, 33, 33, 33, 23, 23, 35, 35, 35, 23, 23, 10, 10, 3, 2, 2, 2, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 158 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000482967277 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000482967277 Building ZINC000483027077 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483027077 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/84 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3cccn3C)cc2)cc1) `ZINC000483027077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483027077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000483027077 none Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3cccn3C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 43, 43, 43, 20, 20, 20, 10, 8, 15, 15, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 43, 43, 43, 20, 15, 15, 8, 8, 2, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50] 50 rigid atoms, others: [54, 50, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 55, 56, 57, 58]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/85 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/85' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@]([O-])([SiH3])c3cccn3C)cc2)cc1) `ZINC000483027077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483027077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000483027077 none Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@]([O-])([SiH3])c3cccn3C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 41, 41, 41, 19, 19, 19, 14, 14, 14, 14, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 41, 19, 14, 14, 7, 7, 2, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50] 50 rigid atoms, others: [54, 50, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 55, 56, 57, 58]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483027077 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077 Building ZINC000483027077 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483027077 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 84) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/84: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3cccn3C)cc2)cc1) `ZINC000483027077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483027077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000483027077 none Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3cccn3C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 43, 43, 43, 20, 20, 20, 10, 8, 15, 15, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 43, 43, 43, 20, 15, 15, 8, 8, 2, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50] 50 rigid atoms, others: [54, 50, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 55, 56, 57, 58]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 85) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/85: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@]([O-])([SiH3])c3cccn3C)cc2)cc1) `ZINC000483027077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483027077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000483027077 none Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@]([O-])([SiH3])c3cccn3C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 41, 41, 41, 19, 19, 19, 14, 14, 14, 14, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 41, 19, 14, 14, 7, 7, 2, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50] 50 rigid atoms, others: [54, 50, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 55, 56, 57, 58]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483027077 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483027077 Building ZINC000483061342 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483061342 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/86 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1csc(C2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)n1) `ZINC000483061342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483061342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000483061342 none COc1ccccc1c1csc(C2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 36, 37, 37, 18, 18, 18, 18, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 18, 37, 37, 37, 37, 37, 37, 37, 18, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/87 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1csc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)n1) `ZINC000483061342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483061342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000483061342 none COc1ccccc1c1csc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 17, 17, 17, 17, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 17, 33, 33, 33, 33, 33, 33, 33, 17, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483061342 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342 Building ZINC000483061342 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483061342 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 86) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/86: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1csc(C2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)n1) `ZINC000483061342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483061342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000483061342 none COc1ccccc1c1csc(C2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 36, 37, 37, 18, 18, 18, 18, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 18, 37, 37, 37, 37, 37, 37, 37, 18, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 87) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/87: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1csc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)n1) `ZINC000483061342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483061342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000483061342 none COc1ccccc1c1csc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 17, 17, 17, 17, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 17, 33, 33, 33, 33, 33, 33, 33, 17, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483061342 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483061342 Building ZINC000483106706 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483106706 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/88 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOc2ncccc21) `ZINC000483106706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483106706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000483106706 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOc2ncccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 31, 31, 11, 31, 31, 31, 31, 31, 31, 4, 4, 1, 1, 1, 3, 6, 9, 10, 10, 10, 10, 10, 10, 10, 10, 9, 4, 4, 4, 31, 31, 15, 31, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 90 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/89 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOc2ncccc21) `ZINC000483106706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483106706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000483106706 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOc2ncccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 29, 29, 4, 29, 29, 29, 29, 29, 29, 4, 4, 1, 1, 1, 3, 7, 10, 11, 11, 11, 11, 11, 11, 11, 11, 10, 4, 4, 4, 29, 29, 4, 29, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 90 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483106706 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706 Building ZINC000483106706 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483106706 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 88) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/88: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOc2ncccc21) `ZINC000483106706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483106706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000483106706 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOc2ncccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 31, 31, 11, 31, 31, 31, 31, 31, 31, 4, 4, 1, 1, 1, 3, 6, 9, 10, 10, 10, 10, 10, 10, 10, 10, 9, 4, 4, 4, 31, 31, 15, 31, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 90 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 89) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/89: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOc2ncccc21) `ZINC000483106706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483106706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000483106706 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOc2ncccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 29, 29, 4, 29, 29, 29, 29, 29, 29, 4, 4, 1, 1, 1, 3, 7, 10, 11, 11, 11, 11, 11, 11, 11, 11, 10, 4, 4, 4, 29, 29, 4, 29, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 90 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483106706 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483106706 Building ZINC000760595263 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760595263 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/90 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(N(C)C(=O)c3ccncc3)cc2)cc1Cl) `ZINC000760595263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760595263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000760595263 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(N(C)C(=O)c3ccncc3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 5, 5, 26, 26, 32, 32, 32, 32, 32, 32, 32, 8, 8, 2, 2, 2, 5, 5, 5, 2, 2, 1, 5, 5, 8, 8, 26, 26, 26, 32, 32, 32, 32, 8, 8, 2] 50 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/91 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(N(C)C(=O)c3ccncc3)cc2)cc1Cl) `ZINC000760595263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760595263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000760595263 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(N(C)C(=O)c3ccncc3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 24, 24, 31, 31, 31, 31, 31, 31, 31, 8, 8, 2, 2, 2, 5, 5, 5, 2, 2, 1, 5, 5, 8, 8, 24, 24, 24, 31, 31, 31, 31, 8, 8, 2] 50 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760595263 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263 Building ZINC000760595263 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760595263 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 90) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/90: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(N(C)C(=O)c3ccncc3)cc2)cc1Cl) `ZINC000760595263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760595263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000760595263 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(N(C)C(=O)c3ccncc3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 5, 5, 26, 26, 32, 32, 32, 32, 32, 32, 32, 8, 8, 2, 2, 2, 5, 5, 5, 2, 2, 1, 5, 5, 8, 8, 26, 26, 26, 32, 32, 32, 32, 8, 8, 2] 50 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 91) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/91: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(N(C)C(=O)c3ccncc3)cc2)cc1Cl) `ZINC000760595263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760595263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000760595263 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(N(C)C(=O)c3ccncc3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 24, 24, 31, 31, 31, 31, 31, 31, 31, 8, 8, 2, 2, 2, 5, 5, 5, 2, 2, 1, 5, 5, 8, 8, 24, 24, 24, 31, 31, 31, 31, 8, 8, 2] 50 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760595263 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760595263 Building ZINC000483297763 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483297763 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/92 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccccc1) `ZINC000483297763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483297763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483297763 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 4, 4, 4, 7, 7, 12, 7, 9, 9, 7, 9, 9, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 4, 12, 12, 36, 9, 9, 8, 9, 9] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 140 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/93 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/93' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccccc1) `ZINC000483297763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483297763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483297763 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 19, 19, 3, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 11, 5, 8, 8, 8, 8, 8, 3, 3, 3, 19, 19, 3, 19, 3, 3, 3, 3, 11, 11, 33, 8, 8, 8, 8, 8] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 132 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483297763 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763 Building ZINC000483297763 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483297763 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 92) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccccc1) `ZINC000483297763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483297763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483297763 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 4, 4, 4, 7, 7, 12, 7, 9, 9, 7, 9, 9, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 4, 12, 12, 36, 9, 9, 8, 9, 9] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 140 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 93) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccccc1) `ZINC000483297763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483297763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483297763 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 19, 19, 3, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 11, 5, 8, 8, 8, 8, 8, 3, 3, 3, 19, 19, 3, 19, 3, 3, 3, 3, 11, 11, 33, 8, 8, 8, 8, 8] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 132 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483297763 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483297763 Building ZINC000483333482 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483333482 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/94 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1cccc(F)c1) `ZINC000483333482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483333482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483333482 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 4, 4, 5, 4, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 3, 5, 5, 15, 10, 10, 10, 10] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 80 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/95 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/95' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1cccc(F)c1) `ZINC000483333482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483333482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483333482 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 7, 5, 10, 10, 10, 10, 10, 10, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 7, 7, 21, 10, 10, 10, 10] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 80 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483333482 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482 Building ZINC000483333482 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483333482 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 94) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/94: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1cccc(F)c1) `ZINC000483333482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483333482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483333482 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 4, 4, 5, 4, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 3, 5, 5, 15, 10, 10, 10, 10] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 80 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 95) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/95: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1cccc(F)c1) `ZINC000483333482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483333482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483333482 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 7, 5, 10, 10, 10, 10, 10, 10, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 7, 7, 21, 10, 10, 10, 10] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 80 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483333482 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333482 Building ZINC000483333488 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483333488 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/96 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1cccc(F)c1) `ZINC000483333488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483333488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483333488 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 4, 4, 4, 6, 6, 8, 6, 12, 12, 12, 12, 12, 12, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 8, 8, 24, 12, 12, 12, 12] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 87 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/97 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/97' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1cccc(F)c1) `ZINC000483333488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483333488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483333488 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 4, 4, 5, 4, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 5, 5, 15, 10, 10, 10, 10] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 74 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483333488 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488 Building ZINC000483333488 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483333488 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 96) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/96: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1cccc(F)c1) `ZINC000483333488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483333488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483333488 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 4, 4, 4, 6, 6, 8, 6, 12, 12, 12, 12, 12, 12, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 8, 8, 24, 12, 12, 12, 12] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 87 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 97) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/97: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1cccc(F)c1) `ZINC000483333488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483333488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483333488 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 4, 4, 5, 4, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 5, 5, 15, 10, 10, 10, 10] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 74 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483333488 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483333488 Building ZINC000483335518 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483335518 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/98 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccc(F)cc1) `ZINC000483335518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483335518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483335518 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 23, 23, 4, 23, 23, 23, 23, 23, 23, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 9, 5, 8, 8, 6, 7, 8, 8, 4, 4, 4, 23, 23, 4, 23, 4, 4, 4, 3, 9, 9, 27, 8, 8, 8, 8] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 129 number of broken/clashed sets: 102 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/99 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/99' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccc(F)cc1) `ZINC000483335518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483335518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483335518 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 4, 4, 4, 6, 6, 12, 6, 8, 8, 8, 8, 8, 8, 4, 4, 4, 21, 21, 6, 21, 4, 4, 4, 4, 12, 12, 36, 8, 8, 8, 8] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483335518 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518 Building ZINC000483335518 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483335518 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 98) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccc(F)cc1) `ZINC000483335518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483335518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483335518 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 23, 23, 4, 23, 23, 23, 23, 23, 23, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 9, 5, 8, 8, 6, 7, 8, 8, 4, 4, 4, 23, 23, 4, 23, 4, 4, 4, 3, 9, 9, 27, 8, 8, 8, 8] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 129 number of broken/clashed sets: 102 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 99) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccc(F)cc1) `ZINC000483335518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483335518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483335518 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 4, 4, 4, 6, 6, 12, 6, 8, 8, 8, 8, 8, 8, 4, 4, 4, 21, 21, 6, 21, 4, 4, 4, 4, 12, 12, 36, 8, 8, 8, 8] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483335518 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335518 Building ZINC000483335520 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483335520 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/100 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccc(F)cc1) `ZINC000483335520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483335520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483335520 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 22, 22, 4, 22, 22, 22, 22, 22, 22, 4, 4, 1, 1, 1, 1, 4, 4, 4, 6, 6, 12, 6, 8, 8, 6, 8, 8, 8, 4, 4, 4, 22, 22, 4, 22, 4, 4, 4, 4, 12, 12, 36, 8, 8, 8, 8] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 153 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/101 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccc(F)cc1) `ZINC000483335520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483335520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483335520 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 19, 19, 3, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 11, 5, 8, 8, 5, 5, 8, 8, 3, 3, 3, 19, 19, 4, 19, 3, 3, 3, 3, 11, 11, 33, 8, 8, 8, 8] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483335520 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520 Building ZINC000483335520 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483335520 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 100) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/100: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccc(F)cc1) `ZINC000483335520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483335520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483335520 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 22, 22, 4, 22, 22, 22, 22, 22, 22, 4, 4, 1, 1, 1, 1, 4, 4, 4, 6, 6, 12, 6, 8, 8, 6, 8, 8, 8, 4, 4, 4, 22, 22, 4, 22, 4, 4, 4, 4, 12, 12, 36, 8, 8, 8, 8] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 153 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 101) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/101: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccc(F)cc1) `ZINC000483335520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483335520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483335520 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 19, 19, 3, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 11, 5, 8, 8, 5, 5, 8, 8, 3, 3, 3, 19, 19, 4, 19, 3, 3, 3, 3, 11, 11, 33, 8, 8, 8, 8] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483335520 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483335520 Building ZINC000760596087 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760596087 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/102 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C)c(S(=O)(=O)NC(C)(C)C)c2)cc1Cl) `ZINC000760596087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760596087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000760596087 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C)c(S(=O)(=O)NC(C)(C)C)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 10, 2, 8, 10, 10, 16, 16, 16, 24, 25, 25, 25, 10, 4, 4, 4, 8, 8, 8, 4, 4, 2, 10, 10, 10, 10, 10, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/103 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C)c(S(=O)(=O)NC(C)(C)C)c2)cc1Cl) `ZINC000760596087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760596087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000760596087 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C)c(S(=O)(=O)NC(C)(C)C)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 16, 16, 16, 25, 25, 25, 25, 10, 4, 4, 4, 8, 8, 8, 4, 4, 2, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760596087 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087 Building ZINC000760596087 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760596087 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 102) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/102: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C)c(S(=O)(=O)NC(C)(C)C)c2)cc1Cl) `ZINC000760596087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760596087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000760596087 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C)c(S(=O)(=O)NC(C)(C)C)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 10, 2, 8, 10, 10, 16, 16, 16, 24, 25, 25, 25, 10, 4, 4, 4, 8, 8, 8, 4, 4, 2, 10, 10, 10, 10, 10, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 103) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/103: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C)c(S(=O)(=O)NC(C)(C)C)c2)cc1Cl) `ZINC000760596087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760596087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000760596087 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C)c(S(=O)(=O)NC(C)(C)C)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 16, 16, 16, 25, 25, 25, 25, 10, 4, 4, 4, 8, 8, 8, 4, 4, 2, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760596087 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760596087 Building ZINC000483636809 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000483636809 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/104 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483636809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636809 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 16, 28, 28, 29, 29, 28, 28, 29, 29, 37, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 4, 16, 16, 29, 29, 29, 29, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/105 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483636809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636809 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 14, 28, 28, 29, 29, 28, 29, 29, 29, 34, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 3, 14, 14, 29, 29, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/106 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/106' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636809.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000483636809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636809 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 16, 28, 28, 29, 29, 28, 28, 29, 29, 37, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 4, 16, 16, 29, 29, 29, 29, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/107 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/107' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636809.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000483636809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636809 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 14, 28, 28, 29, 29, 28, 29, 29, 29, 34, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 3, 14, 14, 29, 29, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483636809 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 Building ZINC000483636809 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000483636809 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 104) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/104: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483636809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636809 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 16, 28, 28, 29, 29, 28, 28, 29, 29, 37, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 4, 16, 16, 29, 29, 29, 29, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 105) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/105: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483636809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636809 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 14, 28, 28, 29, 29, 28, 29, 29, 29, 34, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 3, 14, 14, 29, 29, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 106) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636809.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000483636809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636809 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 16, 28, 28, 29, 29, 28, 28, 29, 29, 37, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 4, 16, 16, 29, 29, 29, 29, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 107) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/107: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636809.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000483636809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636809 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 14, 28, 28, 29, 29, 28, 29, 29, 29, 34, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 3, 14, 14, 29, 29, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483636809 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 Building ZINC000483636809 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000483636809 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 104) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/104: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483636809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636809 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 16, 28, 28, 29, 29, 28, 28, 29, 29, 37, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 4, 16, 16, 29, 29, 29, 29, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 105) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/105: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483636809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636809 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 14, 28, 28, 29, 29, 28, 29, 29, 29, 34, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 3, 14, 14, 29, 29, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 106) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636809.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000483636809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636809 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 16, 28, 28, 29, 29, 28, 28, 29, 29, 37, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 4, 16, 16, 29, 29, 29, 29, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 107) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/107: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636809.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000483636809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636809 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 14, 28, 28, 29, 29, 28, 29, 29, 29, 34, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 3, 14, 14, 29, 29, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483636809 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 Building ZINC000483636809 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000483636809 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 104) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/104: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483636809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636809 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 16, 28, 28, 29, 29, 28, 28, 29, 29, 37, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 4, 16, 16, 29, 29, 29, 29, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 105) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/105: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483636809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636809 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 14, 28, 28, 29, 29, 28, 29, 29, 29, 34, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 3, 14, 14, 29, 29, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 106) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636809.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000483636809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636809 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 16, 28, 28, 29, 29, 28, 28, 29, 29, 37, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 4, 16, 16, 29, 29, 29, 29, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 107) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/107: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636809.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000483636809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636809 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 14, 28, 28, 29, 29, 28, 29, 29, 29, 34, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 3, 14, 14, 29, 29, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483636809 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636809 Building ZINC000483636811 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000483636811 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/108 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483636811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636811 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 15, 28, 28, 29, 29, 28, 28, 29, 29, 34, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 3, 15, 15, 29, 29, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/109 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/109' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483636811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636811 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 16, 27, 27, 30, 30, 27, 28, 30, 30, 36, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 4, 16, 16, 30, 30, 30, 30, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/110 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/110' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636811.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000483636811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636811 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 15, 28, 28, 29, 29, 28, 28, 29, 29, 34, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 3, 15, 15, 29, 29, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/111 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/111' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636811.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000483636811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636811 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 16, 27, 27, 30, 30, 27, 28, 30, 30, 36, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 4, 16, 16, 30, 30, 30, 30, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483636811 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 Building ZINC000483636811 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000483636811 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 108) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483636811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636811 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 15, 28, 28, 29, 29, 28, 28, 29, 29, 34, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 3, 15, 15, 29, 29, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 109) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483636811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636811 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 16, 27, 27, 30, 30, 27, 28, 30, 30, 36, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 4, 16, 16, 30, 30, 30, 30, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 110) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/110: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636811.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000483636811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636811 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 15, 28, 28, 29, 29, 28, 28, 29, 29, 34, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 3, 15, 15, 29, 29, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 111) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/111: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636811.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000483636811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636811 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 16, 27, 27, 30, 30, 27, 28, 30, 30, 36, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 4, 16, 16, 30, 30, 30, 30, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483636811 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 Building ZINC000483636811 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000483636811 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 108) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483636811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636811 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 15, 28, 28, 29, 29, 28, 28, 29, 29, 34, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 3, 15, 15, 29, 29, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 109) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483636811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636811 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 16, 27, 27, 30, 30, 27, 28, 30, 30, 36, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 4, 16, 16, 30, 30, 30, 30, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 110) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/110: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636811.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000483636811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636811 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 15, 28, 28, 29, 29, 28, 28, 29, 29, 34, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 3, 15, 15, 29, 29, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 111) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/111: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636811.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000483636811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636811 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 16, 27, 27, 30, 30, 27, 28, 30, 30, 36, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 4, 16, 16, 30, 30, 30, 30, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483636811 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 Building ZINC000483636811 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000483636811 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 108) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483636811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636811 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 15, 28, 28, 29, 29, 28, 28, 29, 29, 34, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 3, 15, 15, 29, 29, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 109) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483636811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636811 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 16, 27, 27, 30, 30, 27, 28, 30, 30, 36, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 4, 16, 16, 30, 30, 30, 30, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 110) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/110: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636811.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000483636811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636811 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 15, 28, 28, 29, 29, 28, 28, 29, 29, 34, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 3, 15, 15, 29, 29, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 111) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/111: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1) `ZINC000483636811.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000483636811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483636811 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 16, 27, 27, 30, 30, 27, 28, 30, 30, 36, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 4, 16, 16, 30, 30, 30, 30, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483636811 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483636811 Building ZINC000483669576 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483669576 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/112 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)CC(C)(C)C) `ZINC000483669576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483669576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483669576 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)CC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 17, 17, 2, 17, 17, 17, 17, 17, 17, 2, 2, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 7, 7, 7, 7, 7, 2, 2, 2, 17, 17, 2, 17, 2, 2, 2, 4, 11, 11, 33, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 119 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/113 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)CC(C)(C)C) `ZINC000483669576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483669576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483669576 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)CC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 5, 5, 5, 9, 9, 14, 9, 9, 10, 10, 10, 2, 2, 2, 16, 16, 2, 16, 2, 2, 2, 5, 14, 14, 42, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 140 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483669576 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576 Building ZINC000483669576 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483669576 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 112) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/112: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)CC(C)(C)C) `ZINC000483669576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483669576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483669576 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)CC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 17, 17, 2, 17, 17, 17, 17, 17, 17, 2, 2, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 7, 7, 7, 7, 7, 2, 2, 2, 17, 17, 2, 17, 2, 2, 2, 4, 11, 11, 33, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 119 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 113) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)CC(C)(C)C) `ZINC000483669576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483669576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483669576 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)CC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 5, 5, 5, 9, 9, 14, 9, 9, 10, 10, 10, 2, 2, 2, 16, 16, 2, 16, 2, 2, 2, 5, 14, 14, 42, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 140 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483669576 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669576 Building ZINC000483669578 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483669578 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/114 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(C)(C)C) `ZINC000483669578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483669578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483669578 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 5, 5, 5, 9, 9, 14, 9, 9, 9, 9, 9, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 5, 14, 14, 42, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 135 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/115 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(C)(C)C) `ZINC000483669578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483669578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483669578 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 18, 18, 2, 18, 18, 18, 18, 18, 18, 2, 2, 1, 1, 1, 1, 4, 4, 4, 7, 7, 10, 7, 7, 8, 8, 8, 2, 2, 2, 18, 18, 2, 18, 2, 2, 2, 4, 10, 10, 30, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 118 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483669578 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578 Building ZINC000483669578 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483669578 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 114) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/114: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(C)(C)C) `ZINC000483669578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483669578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483669578 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 5, 5, 5, 9, 9, 14, 9, 9, 9, 9, 9, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 5, 14, 14, 42, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 135 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 115) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/115: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(C)(C)C) `ZINC000483669578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483669578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483669578 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 18, 18, 2, 18, 18, 18, 18, 18, 18, 2, 2, 1, 1, 1, 1, 4, 4, 4, 7, 7, 10, 7, 7, 8, 8, 8, 2, 2, 2, 18, 18, 2, 18, 2, 2, 2, 4, 10, 10, 30, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 118 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483669578 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483669578 Building ZINC000483721416 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483721416 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/116 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccccc1) `ZINC000483721416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483721416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483721416 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 11, 5, 8, 8, 5, 8, 8, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 3, 11, 11, 33, 8, 8, 5, 8, 8] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/117 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/117' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccccc1) `ZINC000483721416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483721416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483721416 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 4, 4, 4, 7, 7, 12, 7, 9, 9, 7, 9, 9, 3, 3, 3, 16, 16, 5, 16, 3, 3, 3, 4, 12, 12, 36, 9, 9, 7, 9, 9] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 142 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483721416 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416 Building ZINC000483721416 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483721416 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 116) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccccc1) `ZINC000483721416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483721416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483721416 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 11, 5, 8, 8, 5, 8, 8, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 3, 11, 11, 33, 8, 8, 5, 8, 8] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 117) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccccc1) `ZINC000483721416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483721416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000483721416 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 4, 4, 4, 7, 7, 12, 7, 9, 9, 7, 9, 9, 3, 3, 3, 16, 16, 5, 16, 3, 3, 3, 4, 12, 12, 36, 9, 9, 7, 9, 9] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 142 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483721416 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483721416 Building ZINC000760600105 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760600105 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/118 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)c1ccccc1C(=O)N(C)CCc1ccccc1) `ZINC000760600105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760600105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000760600105 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)c1ccccc1C(=O)N(C)CCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 6, 6, 13, 13, 13, 13, 13, 13, 18, 18, 25, 25, 42, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 13, 13, 13, 13, 25, 25, 25, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/119 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)c1ccccc1C(=O)N(C)CCc1ccccc1) `ZINC000760600105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760600105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000760600105 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)c1ccccc1C(=O)N(C)CCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 7, 7, 15, 15, 15, 15, 15, 15, 21, 21, 28, 28, 43, 43, 43, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 15, 15, 15, 15, 28, 28, 28, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760600105 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105 Building ZINC000760600105 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760600105 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 118) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/118: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)c1ccccc1C(=O)N(C)CCc1ccccc1) `ZINC000760600105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760600105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000760600105 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)c1ccccc1C(=O)N(C)CCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 6, 6, 13, 13, 13, 13, 13, 13, 18, 18, 25, 25, 42, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 13, 13, 13, 13, 25, 25, 25, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 119) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/119: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)c1ccccc1C(=O)N(C)CCc1ccccc1) `ZINC000760600105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760600105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000760600105 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)c1ccccc1C(=O)N(C)CCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 7, 7, 15, 15, 15, 15, 15, 15, 21, 21, 28, 28, 43, 43, 43, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 15, 15, 15, 15, 28, 28, 28, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760600105 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600105 Building ZINC000760600086 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000760600086 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/120 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@H](CN(C)C)CC3)cc2)cc1Cl) `ZINC000760600086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760600086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000760600086 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@H](CN(C)C)CC3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 2, 2, 15, 15, 15, 15, 15, 28, 28, 28, 15, 15, 3, 3, 3, 3, 3, 5, 5, 5, 3, 3, 2, 3, 3, 15, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 15, 15, 3, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/121 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@@H](CN(C)C)CC3)cc2)cc1Cl) `ZINC000760600086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760600086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000760600086 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@@H](CN(C)C)CC3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 15, 15, 15, 15, 15, 28, 28, 28, 15, 15, 3, 3, 3, 3, 3, 5, 5, 5, 3, 3, 2, 3, 3, 15, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 15, 15, 3, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/122 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/122' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@H](CN(C)C)CC3)cc2)cc1Cl) `ZINC000760600086.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000760600086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000760600086 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@H](CN(C)C)CC3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 16, 16, 16, 16, 16, 28, 28, 28, 16, 16, 4, 4, 3, 3, 3, 5, 5, 5, 3, 3, 2, 4, 4, 16, 16, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 16, 16, 16, 16, 4, 4, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/123 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/123' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@@H](CN(C)C)CC3)cc2)cc1Cl) `ZINC000760600086.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000760600086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000760600086 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@@H](CN(C)C)CC3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 2, 2, 15, 15, 15, 15, 15, 28, 28, 28, 15, 15, 3, 3, 3, 3, 3, 5, 5, 5, 3, 3, 2, 3, 3, 15, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 15, 15, 3, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760600086 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 Building ZINC000760600086 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000760600086 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 120) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@H](CN(C)C)CC3)cc2)cc1Cl) `ZINC000760600086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760600086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000760600086 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@H](CN(C)C)CC3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 2, 2, 15, 15, 15, 15, 15, 28, 28, 28, 15, 15, 3, 3, 3, 3, 3, 5, 5, 5, 3, 3, 2, 3, 3, 15, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 15, 15, 3, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 121) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@@H](CN(C)C)CC3)cc2)cc1Cl) `ZINC000760600086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760600086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000760600086 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@@H](CN(C)C)CC3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 15, 15, 15, 15, 15, 28, 28, 28, 15, 15, 3, 3, 3, 3, 3, 5, 5, 5, 3, 3, 2, 3, 3, 15, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 15, 15, 3, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 122) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/122: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@H](CN(C)C)CC3)cc2)cc1Cl) `ZINC000760600086.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000760600086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000760600086 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@H](CN(C)C)CC3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 16, 16, 16, 16, 16, 28, 28, 28, 16, 16, 4, 4, 3, 3, 3, 5, 5, 5, 3, 3, 2, 4, 4, 16, 16, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 16, 16, 16, 16, 4, 4, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 123) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/123: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@@H](CN(C)C)CC3)cc2)cc1Cl) `ZINC000760600086.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000760600086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000760600086 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@@H](CN(C)C)CC3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 2, 2, 15, 15, 15, 15, 15, 28, 28, 28, 15, 15, 3, 3, 3, 3, 3, 5, 5, 5, 3, 3, 2, 3, 3, 15, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 15, 15, 3, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760600086 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 Building ZINC000760600086 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000760600086 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 120) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@H](CN(C)C)CC3)cc2)cc1Cl) `ZINC000760600086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760600086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000760600086 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@H](CN(C)C)CC3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 2, 2, 15, 15, 15, 15, 15, 28, 28, 28, 15, 15, 3, 3, 3, 3, 3, 5, 5, 5, 3, 3, 2, 3, 3, 15, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 15, 15, 3, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 121) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@@H](CN(C)C)CC3)cc2)cc1Cl) `ZINC000760600086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760600086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000760600086 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@@H](CN(C)C)CC3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 15, 15, 15, 15, 15, 28, 28, 28, 15, 15, 3, 3, 3, 3, 3, 5, 5, 5, 3, 3, 2, 3, 3, 15, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 15, 15, 3, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 122) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/122: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@H](CN(C)C)CC3)cc2)cc1Cl) `ZINC000760600086.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000760600086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000760600086 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@H](CN(C)C)CC3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 16, 16, 16, 16, 16, 28, 28, 28, 16, 16, 4, 4, 3, 3, 3, 5, 5, 5, 3, 3, 2, 4, 4, 16, 16, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 16, 16, 16, 16, 4, 4, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 123) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/123: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@@H](CN(C)C)CC3)cc2)cc1Cl) `ZINC000760600086.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000760600086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000760600086 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@@H](CN(C)C)CC3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 2, 2, 15, 15, 15, 15, 15, 28, 28, 28, 15, 15, 3, 3, 3, 3, 3, 5, 5, 5, 3, 3, 2, 3, 3, 15, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 15, 15, 3, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760600086 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 Building ZINC000760600086 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000760600086 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 120) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@H](CN(C)C)CC3)cc2)cc1Cl) `ZINC000760600086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760600086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000760600086 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@H](CN(C)C)CC3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 2, 2, 15, 15, 15, 15, 15, 28, 28, 28, 15, 15, 3, 3, 3, 3, 3, 5, 5, 5, 3, 3, 2, 3, 3, 15, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 15, 15, 3, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 121) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@@H](CN(C)C)CC3)cc2)cc1Cl) `ZINC000760600086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760600086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000760600086 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@@H](CN(C)C)CC3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 15, 15, 15, 15, 15, 28, 28, 28, 15, 15, 3, 3, 3, 3, 3, 5, 5, 5, 3, 3, 2, 3, 3, 15, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 15, 15, 3, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 122) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/122: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@H](CN(C)C)CC3)cc2)cc1Cl) `ZINC000760600086.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000760600086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000760600086 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@H](CN(C)C)CC3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 16, 16, 16, 16, 16, 28, 28, 28, 16, 16, 4, 4, 3, 3, 3, 5, 5, 5, 3, 3, 2, 4, 4, 16, 16, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 16, 16, 16, 16, 4, 4, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 123) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/123: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@@H](CN(C)C)CC3)cc2)cc1Cl) `ZINC000760600086.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000760600086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000760600086 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[C@@H](CN(C)C)CC3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 2, 2, 15, 15, 15, 15, 15, 28, 28, 28, 15, 15, 3, 3, 3, 3, 3, 5, 5, 5, 3, 3, 2, 3, 3, 15, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 15, 15, 3, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760600086 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760600086 Building ZINC000483948365 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483948365 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/124 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)c1c(C)nn(c2ccc(F)cc2)c1C) `ZINC000483948365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483948365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483948365 none CCOC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)c1c(C)nn(c2ccc(F)cc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 10, 9, 8, 9, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 8, 19, 19, 19, 19, 19, 33, 33, 19, 33, 33, 33, 19, 19, 21, 21, 21, 21, 21, 4, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 33, 33, 33, 33, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/125 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/125' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)c1c(C)nn(c2ccc(F)cc2)c1C) `ZINC000483948365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483948365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483948365 none CCOC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)c1c(C)nn(c2ccc(F)cc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 10, 8, 7, 8, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 17, 17, 17, 17, 17, 33, 33, 17, 33, 33, 33, 17, 17, 20, 20, 20, 20, 20, 4, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 33, 33, 33, 33, 17, 17, 17] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483948365 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365 Building ZINC000483948365 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483948365 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 124) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)c1c(C)nn(c2ccc(F)cc2)c1C) `ZINC000483948365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483948365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483948365 none CCOC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)c1c(C)nn(c2ccc(F)cc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 10, 9, 8, 9, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 8, 19, 19, 19, 19, 19, 33, 33, 19, 33, 33, 33, 19, 19, 21, 21, 21, 21, 21, 4, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 33, 33, 33, 33, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 125) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)c1c(C)nn(c2ccc(F)cc2)c1C) `ZINC000483948365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483948365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483948365 none CCOC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)c1c(C)nn(c2ccc(F)cc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 10, 8, 7, 8, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 17, 17, 17, 17, 17, 33, 33, 17, 33, 33, 33, 17, 17, 20, 20, 20, 20, 20, 4, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 33, 33, 33, 33, 17, 17, 17] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483948365 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948365 Building ZINC000483948373 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483948373 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/126 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)c1c(C)nn(c2ccc(F)cc2)c1C) `ZINC000483948373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483948373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483948373 none CCOC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)c1c(C)nn(c2ccc(F)cc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 10, 8, 7, 8, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 17, 17, 17, 17, 17, 33, 33, 17, 17, 33, 33, 17, 17, 20, 20, 20, 20, 20, 4, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 33, 33, 33, 33, 17, 17, 17] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/127 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)c1c(C)nn(c2ccc(F)cc2)c1C) `ZINC000483948373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483948373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483948373 none CCOC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)c1c(C)nn(c2ccc(F)cc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 10, 9, 8, 9, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 8, 19, 19, 19, 19, 19, 33, 33, 19, 19, 33, 33, 19, 19, 21, 21, 21, 21, 21, 4, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 33, 33, 33, 33, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483948373 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373 Building ZINC000483948373 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483948373 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 126) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/126: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)c1c(C)nn(c2ccc(F)cc2)c1C) `ZINC000483948373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483948373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483948373 none CCOC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)c1c(C)nn(c2ccc(F)cc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 10, 8, 7, 8, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 17, 17, 17, 17, 17, 33, 33, 17, 17, 33, 33, 17, 17, 20, 20, 20, 20, 20, 4, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 33, 33, 33, 33, 17, 17, 17] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 127) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/127: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)c1c(C)nn(c2ccc(F)cc2)c1C) `ZINC000483948373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483948373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483948373 none CCOC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)c1c(C)nn(c2ccc(F)cc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 10, 9, 8, 9, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 8, 19, 19, 19, 19, 19, 33, 33, 19, 19, 33, 33, 19, 19, 21, 21, 21, 21, 21, 4, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 33, 33, 33, 33, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483948373 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483948373 Building ZINC000483978467 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483978467 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/128 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cn2cnc3ccccc32)c2ccc(F)cc2)cn1) `ZINC000483978467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483978467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483978467 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cn2cnc3ccccc32)c2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 10, 7, 7, 1, 1, 1, 1, 3, 3, 3, 5, 5, 11, 22, 22, 22, 22, 22, 22, 22, 22, 5, 6, 6, 5, 5, 6, 6, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 3, 11, 11, 22, 22, 22, 22, 22, 6, 6, 6, 6, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 97 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/129 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](Cn2cnc3ccccc32)c2ccc(F)cc2)cn1) `ZINC000483978467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483978467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483978467 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](Cn2cnc3ccccc32)c2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 11, 24, 24, 24, 24, 24, 24, 24, 24, 5, 7, 7, 5, 5, 7, 7, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 3, 11, 11, 24, 24, 24, 24, 24, 7, 7, 7, 7, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483978467 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467 Building ZINC000483978467 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483978467 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 128) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cn2cnc3ccccc32)c2ccc(F)cc2)cn1) `ZINC000483978467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483978467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483978467 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cn2cnc3ccccc32)c2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 10, 7, 7, 1, 1, 1, 1, 3, 3, 3, 5, 5, 11, 22, 22, 22, 22, 22, 22, 22, 22, 5, 6, 6, 5, 5, 6, 6, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 3, 11, 11, 22, 22, 22, 22, 22, 6, 6, 6, 6, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 97 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 129) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](Cn2cnc3ccccc32)c2ccc(F)cc2)cn1) `ZINC000483978467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483978467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483978467 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](Cn2cnc3ccccc32)c2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 11, 24, 24, 24, 24, 24, 24, 24, 24, 5, 7, 7, 5, 5, 7, 7, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 3, 11, 11, 24, 24, 24, 24, 24, 7, 7, 7, 7, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483978467 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978467 Building ZINC000483978473 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483978473 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/130 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](Cn2cnc3ccccc32)c2ccc(F)cc2)cn1) `ZINC000483978473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483978473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483978473 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](Cn2cnc3ccccc32)c2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 11, 24, 24, 24, 24, 24, 24, 24, 24, 5, 7, 7, 5, 5, 7, 7, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 3, 11, 11, 24, 24, 24, 24, 24, 7, 7, 7, 7, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/131 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](Cn2cnc3ccccc32)c2ccc(F)cc2)cn1) `ZINC000483978473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483978473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483978473 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](Cn2cnc3ccccc32)c2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 11, 22, 22, 22, 22, 22, 22, 22, 22, 5, 6, 6, 5, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 3, 11, 11, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 92 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483978473 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473 Building ZINC000483978473 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000483978473 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 130) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/130: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](Cn2cnc3ccccc32)c2ccc(F)cc2)cn1) `ZINC000483978473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000483978473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483978473 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](Cn2cnc3ccccc32)c2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 11, 24, 24, 24, 24, 24, 24, 24, 24, 5, 7, 7, 5, 5, 7, 7, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 3, 11, 11, 24, 24, 24, 24, 24, 7, 7, 7, 7, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 131) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/131: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](Cn2cnc3ccccc32)c2ccc(F)cc2)cn1) `ZINC000483978473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000483978473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000483978473 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](Cn2cnc3ccccc32)c2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 11, 22, 22, 22, 22, 22, 22, 22, 22, 5, 6, 6, 5, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 3, 11, 11, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 92 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000483978473 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000483978473 Building ZINC000484032884 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000484032884 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/132 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccco2)n[nH]1) `ZINC000484032884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000484032884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000484032884 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccco2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 12, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 4, 4, 4, 3, 3, 3, 14, 14, 6, 14, 3, 3, 3, 4, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 59 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/133 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccco2)n[nH]1) `ZINC000484032884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000484032884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000484032884 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccco2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 12, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 4, 4, 4, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 4, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000484032884 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884 Building ZINC000484032884 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000484032884 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 132) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/132: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccco2)n[nH]1) `ZINC000484032884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000484032884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000484032884 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccco2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 12, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 4, 4, 4, 3, 3, 3, 14, 14, 6, 14, 3, 3, 3, 4, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 59 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 133) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/133: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccco2)n[nH]1) `ZINC000484032884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000484032884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000484032884 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccco2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 12, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 4, 4, 4, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 4, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000484032884 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484032884 Building ZINC000484275863 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000484275863 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/134 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(C(=O)NCc2ccccc2F)c1) `ZINC000484275863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000484275863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000484275863 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(C(=O)NCc2ccccc2F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 12, 12, 12, 43, 48, 48, 48, 48, 48, 48, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 12, 43, 43, 48, 48, 48, 48, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/135 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(C(=O)NCc2ccccc2F)c1) `ZINC000484275863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000484275863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000484275863 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(C(=O)NCc2ccccc2F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 12, 12, 12, 42, 48, 48, 48, 48, 48, 48, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 12, 42, 42, 48, 48, 48, 48, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000484275863 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863 Building ZINC000484275863 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000484275863 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 134) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/134: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(C(=O)NCc2ccccc2F)c1) `ZINC000484275863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000484275863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000484275863 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(C(=O)NCc2ccccc2F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 12, 12, 12, 43, 48, 48, 48, 48, 48, 48, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 12, 43, 43, 48, 48, 48, 48, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 135) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/135: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(C(=O)NCc2ccccc2F)c1) `ZINC000484275863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000484275863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000484275863 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(C(=O)NCc2ccccc2F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 12, 12, 12, 42, 48, 48, 48, 48, 48, 48, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 12, 42, 42, 48, 48, 48, 48, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000484275863 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484275863 Building ZINC000484315009 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000484315009 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/136 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1sc2c(c1C(=O)c1ccncc1)CCC2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000484315009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000484315009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000484315009 none O=C(Nc1sc2c(c1C(=O)c1ccncc1)CCC2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 8, 1, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 12, 12, 12, 12, 12, 22, 22, 24, 24, 22, 24, 24, 12, 12, 12, 1, 1, 1, 8, 8, 8, 8, 12, 12, 8, 12, 12, 8, 4, 24, 24, 24, 24, 12, 12, 12, 12, 12, 12, 8, 12, 12, 8, 12, 12, 8] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/137 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1sc2c(c1C(=O)c1ccncc1)CCC2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000484315009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000484315009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000484315009 none O=C(Nc1sc2c(c1C(=O)c1ccncc1)CCC2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 8, 1, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 13, 13, 13, 13, 13, 23, 23, 25, 25, 23, 25, 25, 13, 13, 13, 1, 1, 1, 8, 8, 8, 8, 11, 11, 8, 11, 11, 8, 4, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 8, 11, 11, 8, 11, 11, 8] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000484315009 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009 Building ZINC000484315009 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000484315009 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 136) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/136: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1sc2c(c1C(=O)c1ccncc1)CCC2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000484315009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000484315009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000484315009 none O=C(Nc1sc2c(c1C(=O)c1ccncc1)CCC2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 8, 1, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 12, 12, 12, 12, 12, 22, 22, 24, 24, 22, 24, 24, 12, 12, 12, 1, 1, 1, 8, 8, 8, 8, 12, 12, 8, 12, 12, 8, 4, 24, 24, 24, 24, 12, 12, 12, 12, 12, 12, 8, 12, 12, 8, 12, 12, 8] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 137) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/137: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1sc2c(c1C(=O)c1ccncc1)CCC2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000484315009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000484315009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000484315009 none O=C(Nc1sc2c(c1C(=O)c1ccncc1)CCC2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 8, 1, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 13, 13, 13, 13, 13, 23, 23, 25, 25, 23, 25, 25, 13, 13, 13, 1, 1, 1, 8, 8, 8, 8, 11, 11, 8, 11, 11, 8, 4, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 8, 11, 11, 8, 11, 11, 8] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000484315009 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484315009 Building ZINC001649006616 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001649006616 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/138 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21)C(F)(F)F) `ZINC001649006616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001649006616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649006616 none O=C(NCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 18, 12, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 18, 18, 12, 12, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/139 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21)C(F)(F)F) `ZINC001649006616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001649006616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649006616 none O=C(NCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 15, 11, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 27, 27, 27, 27, 27, 15, 15, 11, 11, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC001649006616 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616 Building ZINC001649006616 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001649006616 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 138) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/138: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21)C(F)(F)F) `ZINC001649006616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001649006616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649006616 none O=C(NCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 18, 12, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 18, 18, 12, 12, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 139) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21)C(F)(F)F) `ZINC001649006616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001649006616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649006616 none O=C(NCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 15, 11, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 27, 27, 27, 27, 27, 15, 15, 11, 11, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC001649006616 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006616 Building ZINC001649006617 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001649006617 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/140 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21)C(F)(F)F) `ZINC001649006617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001649006617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649006617 none O=C(NCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 15, 11, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 15, 15, 11, 11, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/141 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21)C(F)(F)F) `ZINC001649006617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001649006617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649006617 none O=C(NCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 18, 12, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 18, 18, 12, 12, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC001649006617 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617 Building ZINC001649006617 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001649006617 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 140) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21)C(F)(F)F) `ZINC001649006617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001649006617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649006617 none O=C(NCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 15, 11, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 15, 15, 11, 11, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 141) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21)C(F)(F)F) `ZINC001649006617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001649006617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649006617 none O=C(NCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 18, 12, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 18, 18, 12, 12, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC001649006617 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001649006617 Building ZINC000484823326 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000484823326 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/142 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c1ccccc1OC)c1ccc(Br)cc1C) `ZINC000484823326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000484823326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000484823326 none COC(=O)[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c1ccccc1OC)c1ccc(Br)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 26, 38, 10, 26, 26, 4, 1, 4, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 10, 17, 17, 14, 17, 17, 17, 17, 38, 38, 38, 26, 26, 26, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 182 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/143 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/143' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c1ccccc1OC)c1ccc(Br)cc1C) `ZINC000484823326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000484823326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000484823326 none COC(=O)[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c1ccccc1OC)c1ccc(Br)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 27, 42, 13, 27, 27, 5, 1, 5, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 13, 21, 21, 18, 18, 21, 21, 21, 42, 42, 42, 27, 27, 27, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 178 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000484823326 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326 Building ZINC000484823326 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000484823326 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 142) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/142: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c1ccccc1OC)c1ccc(Br)cc1C) `ZINC000484823326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000484823326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000484823326 none COC(=O)[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c1ccccc1OC)c1ccc(Br)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 26, 38, 10, 26, 26, 4, 1, 4, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 10, 17, 17, 14, 17, 17, 17, 17, 38, 38, 38, 26, 26, 26, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 182 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 143) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/143: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c1ccccc1OC)c1ccc(Br)cc1C) `ZINC000484823326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000484823326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000484823326 none COC(=O)[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c1ccccc1OC)c1ccc(Br)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 27, 42, 13, 27, 27, 5, 1, 5, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 13, 21, 21, 18, 18, 21, 21, 21, 42, 42, 42, 27, 27, 27, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 178 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000484823326 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823326 Building ZINC000484823329 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000484823329 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/144 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c1ccccc1OC)c1ccc(Br)cc1C) `ZINC000484823329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000484823329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000484823329 none COC(=O)[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c1ccccc1OC)c1ccc(Br)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 28, 42, 13, 28, 28, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 13, 21, 21, 19, 19, 21, 21, 21, 42, 42, 42, 28, 28, 28, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 174 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/145 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/145' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C)N(C(=O)[C@]([O-])([SiH3])c1ccccc1OC)c1ccc(Br)cc1C) `ZINC000484823329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000484823329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000484823329 none COC(=O)[C@H](C)N(C(=O)[C@]([O-])([SiH3])c1ccccc1OC)c1ccc(Br)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 27, 39, 10, 27, 27, 4, 1, 4, 1, 1, 1, 4, 4, 3, 4, 4, 4, 4, 10, 17, 17, 14, 14, 17, 17, 17, 39, 39, 39, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 174 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000484823329 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329 Building ZINC000484823329 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000484823329 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 144) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/144: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c1ccccc1OC)c1ccc(Br)cc1C) `ZINC000484823329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000484823329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000484823329 none COC(=O)[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c1ccccc1OC)c1ccc(Br)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 28, 42, 13, 28, 28, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 13, 21, 21, 19, 19, 21, 21, 21, 42, 42, 42, 28, 28, 28, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 174 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 145) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/145: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C)N(C(=O)[C@]([O-])([SiH3])c1ccccc1OC)c1ccc(Br)cc1C) `ZINC000484823329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000484823329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000484823329 none COC(=O)[C@H](C)N(C(=O)[C@]([O-])([SiH3])c1ccccc1OC)c1ccc(Br)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 27, 39, 10, 27, 27, 4, 1, 4, 1, 1, 1, 4, 4, 3, 4, 4, 4, 4, 10, 17, 17, 14, 14, 17, 17, 17, 39, 39, 39, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 174 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000484823329 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484823329 Building ZINC000484951028 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000484951028 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/146 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cccc(NC(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccccc3OC)c2)c1) `ZINC000484951028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000484951028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000484951028 none CCOC(=O)c1cccc(NC(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccccc3OC)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 42, 22, 42, 22, 22, 22, 22, 7, 7, 4, 7, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 4, 22, 50, 50, 50, 50, 50, 22, 22, 22, 7, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 22] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/147 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cccc(NC(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccccc3OC)c2)c1) `ZINC000484951028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000484951028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000484951028 none CCOC(=O)c1cccc(NC(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccccc3OC)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 42, 22, 42, 22, 22, 22, 22, 7, 7, 4, 7, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 4, 22, 50, 50, 50, 50, 50, 22, 22, 22, 7, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 22] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000484951028 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028 Building ZINC000484951028 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000484951028 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 146) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/146: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cccc(NC(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccccc3OC)c2)c1) `ZINC000484951028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000484951028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000484951028 none CCOC(=O)c1cccc(NC(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccccc3OC)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 42, 22, 42, 22, 22, 22, 22, 7, 7, 4, 7, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 4, 22, 50, 50, 50, 50, 50, 22, 22, 22, 7, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 22] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 147) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/147: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cccc(NC(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccccc3OC)c2)c1) `ZINC000484951028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000484951028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000484951028 none CCOC(=O)c1cccc(NC(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccccc3OC)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 42, 22, 42, 22, 22, 22, 22, 7, 7, 4, 7, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 4, 22, 50, 50, 50, 50, 50, 22, 22, 22, 7, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 22] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000484951028 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000484951028 Building ZINC000485125237 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485125237 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/148 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)N1CCCC1) `ZINC000485125237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485125237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000485125237 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 4, 4, 4, 13, 13, 7, 13, 13, 13, 16, 34, 34, 34, 34, 34, 34, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 4, 13, 13, 13, 13, 16, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/149 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)N1CCCC1) `ZINC000485125237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485125237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000485125237 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 17, 34, 34, 35, 35, 35, 35, 4, 4, 4, 9, 9, 7, 9, 9, 4, 4, 4, 4, 13, 13, 13, 13, 17, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 123 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485125237 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237 Building ZINC000485125237 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485125237 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 148) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)N1CCCC1) `ZINC000485125237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485125237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000485125237 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 4, 4, 4, 13, 13, 7, 13, 13, 13, 16, 34, 34, 34, 34, 34, 34, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 4, 13, 13, 13, 13, 16, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 149) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/149: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)N1CCCC1) `ZINC000485125237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485125237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000485125237 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 17, 34, 34, 35, 35, 35, 35, 4, 4, 4, 9, 9, 7, 9, 9, 4, 4, 4, 4, 13, 13, 13, 13, 17, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 123 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485125237 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485125237 Building ZINC000485170340 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000485170340 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/150 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485170340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170340 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 19, 21, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/151 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485170340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170340 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 19, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 30 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 54 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/152 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/152' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170340.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000485170340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170340 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 19, 21, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/153 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/153' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170340.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000485170340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170340 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 19, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 30 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 54 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485170340 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 Building ZINC000485170340 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000485170340 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 150) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/150: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485170340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170340 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 19, 21, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 151) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485170340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170340 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 19, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 30 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 54 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 152) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170340.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000485170340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170340 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 19, 21, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 153) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/153: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170340.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000485170340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170340 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 19, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 30 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 54 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485170340 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 Building ZINC000485170340 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000485170340 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 150) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/150: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485170340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170340 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 19, 21, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 151) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485170340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170340 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 19, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 30 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 54 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 152) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170340.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000485170340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170340 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 19, 21, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 153) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/153: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170340.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000485170340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170340 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 19, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 30 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 54 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485170340 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 Building ZINC000485170340 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000485170340 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 150) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/150: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485170340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170340 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 19, 21, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 151) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485170340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170340 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 19, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 30 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 54 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 152) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170340.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000485170340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170340 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 19, 21, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 153) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/153: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170340.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000485170340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170340 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 19, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 30 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 54 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485170340 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170340 Building ZINC000485170352 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000485170352 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/154 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485170352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170352 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 17, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 29 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/155 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485170352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170352 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 16, 18, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 29 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/156 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/156' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170352.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000485170352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170352 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 17, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 29 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/157 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/157' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170352.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000485170352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170352 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 16, 18, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 29 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485170352 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 Building ZINC000485170352 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000485170352 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 154) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/154: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485170352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170352 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 17, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 29 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 155) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/155: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485170352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170352 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 16, 18, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 29 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 156) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/156: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170352.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000485170352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170352 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 17, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 29 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 157) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/157: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170352.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000485170352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170352 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 16, 18, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 29 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485170352 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 Building ZINC000485170352 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000485170352 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 154) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/154: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485170352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170352 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 17, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 29 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 155) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/155: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485170352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170352 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 16, 18, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 29 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 156) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/156: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170352.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000485170352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170352 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 17, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 29 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 157) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/157: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170352.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000485170352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170352 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 16, 18, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 29 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485170352 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 Building ZINC000485170352 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000485170352 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 154) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/154: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485170352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170352 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 17, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 29 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 155) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/155: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485170352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170352 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 16, 18, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 29 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 156) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/156: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170352.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000485170352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170352 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 17, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 29 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 157) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/157: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21) `ZINC000485170352.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000485170352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 Warning: atom stereo specified for planar atom 33 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000485170352 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCCCN2c2cc(Br)c(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 16, 18, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 29 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485170352 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485170352 Building ZINC000485194342 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485194342 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/158 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NS(=O)(=O)Cc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)cc2)cc1) `ZINC000485194342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485194342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000485194342 none COc1ccc(NS(=O)(=O)Cc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 50, 46, 29, 13, 29, 29, 7, 4, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 50, 50, 50, 50, 50, 50, 50, 46, 13, 13, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 50, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/159 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NS(=O)(=O)Cc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)cc2)cc1) `ZINC000485194342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485194342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000485194342 none COc1ccc(NS(=O)(=O)Cc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 50, 50, 47, 31, 14, 31, 31, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 47, 14, 14, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 50, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485194342 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342 Building ZINC000485194342 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485194342 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 158) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/158: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NS(=O)(=O)Cc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)cc2)cc1) `ZINC000485194342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485194342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000485194342 none COc1ccc(NS(=O)(=O)Cc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 50, 46, 29, 13, 29, 29, 7, 4, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 50, 50, 50, 50, 50, 50, 50, 46, 13, 13, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 50, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 159) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NS(=O)(=O)Cc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)cc2)cc1) `ZINC000485194342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485194342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000485194342 none COc1ccc(NS(=O)(=O)Cc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 50, 50, 47, 31, 14, 31, 31, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 47, 14, 14, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 50, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485194342 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485194342 Building ZINC000485290944 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485290944 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/160 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CSCc1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000485290944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485290944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000485290944 none COC(=O)CSCc1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 14, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 32, 41, 18, 10, 4, 4, 2, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 4, 41, 41, 41, 32, 32, 10, 10, 3, 4, 4, 2, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/161 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CSCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000485290944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485290944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000485290944 none COC(=O)CSCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 14, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 34, 42, 18, 9, 3, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 3, 42, 42, 42, 34, 34, 9, 9, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 3] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485290944 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944 Building ZINC000485290944 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485290944 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 160) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CSCc1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000485290944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485290944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000485290944 none COC(=O)CSCc1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 14, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 32, 41, 18, 10, 4, 4, 2, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 4, 41, 41, 41, 32, 32, 10, 10, 3, 4, 4, 2, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 161) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CSCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000485290944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485290944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000485290944 none COC(=O)CSCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 14, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 34, 42, 18, 9, 3, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 3, 42, 42, 42, 34, 34, 9, 9, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 3] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485290944 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485290944 Building ZINC000485279138 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485279138 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/162 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1S(=O)(=O)CC) `ZINC000485279138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485279138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000485279138 none CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1S(=O)(=O)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 4, 6, 6, 3, 3, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 14, 5, 5, 5, 5, 5, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 5, 5, 5, 5, 14, 14, 14, 14, 14] 28 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 75 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/163 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1S(=O)(=O)CC) `ZINC000485279138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485279138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000485279138 none CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1S(=O)(=O)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 18, 6, 6, 6, 6, 6, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 6, 6, 6, 6, 18, 18, 18, 18, 18] 34 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 101 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485279138 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138 Building ZINC000485279138 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485279138 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 162) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1S(=O)(=O)CC) `ZINC000485279138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485279138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000485279138 none CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1S(=O)(=O)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 4, 6, 6, 3, 3, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 14, 5, 5, 5, 5, 5, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 5, 5, 5, 5, 14, 14, 14, 14, 14] 28 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 75 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 163) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/163: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1S(=O)(=O)CC) `ZINC000485279138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485279138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000485279138 none CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1S(=O)(=O)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 18, 6, 6, 6, 6, 6, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 6, 6, 6, 6, 18, 18, 18, 18, 18] 34 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 101 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485279138 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485279138 Building ZINC000485415107 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000485415107 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/164 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cnc(C[N@]2CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C) `ZINC000485415107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485415107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000485415107 none COc1c(C)cnc(C[N@]2CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 13, 13, 13, 13, 4, 13, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 13, 13, 13, 13, 4, 4, 4, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50] 50 rigid atoms, others: [48, 50, 47, 16, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 161 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/165 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cnc(C[N@]2CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C) `ZINC000485415107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485415107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000485415107 none COc1c(C)cnc(C[N@]2CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 13, 13, 13, 13, 4, 13, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 13, 13, 13, 13, 4, 4, 4, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50] 50 rigid atoms, others: [48, 50, 47, 16, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 161 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/166 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/166' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cnc(C[N@]2CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C) `ZINC000485415107.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000485415107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000485415107 none COc1c(C)cnc(C[N@]2CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 14, 14, 14, 14, 3, 14, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 14, 14, 14, 14, 3, 3, 3, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50] 50 rigid atoms, others: [48, 50, 47, 16, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 167 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/167 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/167' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cnc(C[N@]2CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C) `ZINC000485415107.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000485415107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000485415107 none COc1c(C)cnc(C[N@]2CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 14, 14, 14, 14, 3, 14, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 14, 14, 14, 14, 3, 3, 3, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50] 50 rigid atoms, others: [48, 50, 47, 16, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 167 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485415107 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 Building ZINC000485415107 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000485415107 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 164) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/164: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cnc(C[N@]2CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C) `ZINC000485415107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485415107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000485415107 none COc1c(C)cnc(C[N@]2CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 13, 13, 13, 13, 4, 13, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 13, 13, 13, 13, 4, 4, 4, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50] 50 rigid atoms, others: [48, 50, 47, 16, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 161 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 165) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cnc(C[N@]2CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C) `ZINC000485415107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485415107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000485415107 none COc1c(C)cnc(C[N@]2CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 13, 13, 13, 13, 4, 13, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 13, 13, 13, 13, 4, 4, 4, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50] 50 rigid atoms, others: [48, 50, 47, 16, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 161 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 166) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cnc(C[N@]2CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C) `ZINC000485415107.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000485415107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000485415107 none COc1c(C)cnc(C[N@]2CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 14, 14, 14, 14, 3, 14, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 14, 14, 14, 14, 3, 3, 3, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50] 50 rigid atoms, others: [48, 50, 47, 16, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 167 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 167) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cnc(C[N@]2CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C) `ZINC000485415107.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000485415107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000485415107 none COc1c(C)cnc(C[N@]2CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 14, 14, 14, 14, 3, 14, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 14, 14, 14, 14, 3, 3, 3, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50] 50 rigid atoms, others: [48, 50, 47, 16, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 167 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485415107 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 Building ZINC000485415107 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000485415107 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 164) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/164: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cnc(C[N@]2CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C) `ZINC000485415107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485415107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000485415107 none COc1c(C)cnc(C[N@]2CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 13, 13, 13, 13, 4, 13, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 13, 13, 13, 13, 4, 4, 4, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50] 50 rigid atoms, others: [48, 50, 47, 16, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 161 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 165) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cnc(C[N@]2CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C) `ZINC000485415107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485415107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000485415107 none COc1c(C)cnc(C[N@]2CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 13, 13, 13, 13, 4, 13, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 13, 13, 13, 13, 4, 4, 4, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50] 50 rigid atoms, others: [48, 50, 47, 16, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 161 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 166) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cnc(C[N@]2CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C) `ZINC000485415107.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000485415107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000485415107 none COc1c(C)cnc(C[N@]2CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 14, 14, 14, 14, 3, 14, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 14, 14, 14, 14, 3, 3, 3, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50] 50 rigid atoms, others: [48, 50, 47, 16, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 167 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 167) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cnc(C[N@]2CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C) `ZINC000485415107.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000485415107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000485415107 none COc1c(C)cnc(C[N@]2CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 14, 14, 14, 14, 3, 14, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 14, 14, 14, 14, 3, 3, 3, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50] 50 rigid atoms, others: [48, 50, 47, 16, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 167 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485415107 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 Building ZINC000485415107 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000485415107 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 164) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/164: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cnc(C[N@]2CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C) `ZINC000485415107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485415107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000485415107 none COc1c(C)cnc(C[N@]2CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 13, 13, 13, 13, 4, 13, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 13, 13, 13, 13, 4, 4, 4, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50] 50 rigid atoms, others: [48, 50, 47, 16, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 161 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 165) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cnc(C[N@]2CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C) `ZINC000485415107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485415107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000485415107 none COc1c(C)cnc(C[N@]2CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 13, 13, 13, 13, 4, 13, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 13, 13, 13, 13, 4, 4, 4, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50] 50 rigid atoms, others: [48, 50, 47, 16, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 161 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 166) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cnc(C[N@]2CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C) `ZINC000485415107.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000485415107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000485415107 none COc1c(C)cnc(C[N@]2CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 14, 14, 14, 14, 3, 14, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 14, 14, 14, 14, 3, 3, 3, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50] 50 rigid atoms, others: [48, 50, 47, 16, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 167 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 167) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C)cnc(C[N@]2CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C) `ZINC000485415107.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000485415107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000485415107 none COc1c(C)cnc(C[N@]2CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 14, 14, 14, 14, 3, 14, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 14, 14, 14, 14, 3, 3, 3, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50] 50 rigid atoms, others: [48, 50, 47, 16, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 167 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485415107 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415107 Building ZINC000485425638 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485425638 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/168 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1cccc(Cl)c1) `ZINC000485425638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485425638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000485425638 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 23, 23, 23, 32, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 12, 32, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/169 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1cccc(Cl)c1) `ZINC000485425638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485425638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000485425638 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 23, 23, 23, 31, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 12, 31, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485425638 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638 Building ZINC000485425638 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485425638 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 168) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/168: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1cccc(Cl)c1) `ZINC000485425638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485425638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000485425638 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 23, 23, 23, 32, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 12, 32, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 169) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1cccc(Cl)c1) `ZINC000485425638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485425638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000485425638 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 23, 23, 23, 31, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 12, 31, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485425638 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485425638 Building ZINC000485415902 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485415902 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/170 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1ccccc1Cl) `ZINC000485415902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485415902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000485415902 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 27, 27, 27, 38, 50, 50, 38, 50, 50, 50, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 10, 38, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/171 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1ccccc1Cl) `ZINC000485415902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485415902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000485415902 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 27, 27, 27, 38, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 10, 38, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485415902 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902 Building ZINC000485415902 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485415902 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 170) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1ccccc1Cl) `ZINC000485415902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485415902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000485415902 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 27, 27, 27, 38, 50, 50, 38, 50, 50, 50, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 10, 38, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 171) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1ccccc1Cl) `ZINC000485415902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485415902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000485415902 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 27, 27, 27, 38, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 10, 38, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485415902 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485415902 Building ZINC000485418552 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485418552 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/172 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1ccc(Cl)cc1) `ZINC000485418552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485418552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000485418552 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 13, 13, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 33, 33, 33, 46, 50, 50, 46, 46, 50, 50, 13, 13, 13, 13, 13, 2, 3, 3, 3, 3, 3, 3, 13, 46, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/173 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/173' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1ccc(Cl)cc1) `ZINC000485418552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485418552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000485418552 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 13, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 13, 13, 13, 32, 32, 32, 46, 49, 49, 46, 46, 49, 49, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 13, 46, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485418552 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552 Building ZINC000485418552 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485418552 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 172) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1ccc(Cl)cc1) `ZINC000485418552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485418552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000485418552 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 13, 13, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 33, 33, 33, 46, 50, 50, 46, 46, 50, 50, 13, 13, 13, 13, 13, 2, 3, 3, 3, 3, 3, 3, 13, 46, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 173) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1ccc(Cl)cc1) `ZINC000485418552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485418552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000485418552 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)cc1S(=O)(=O)Nc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 13, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 13, 13, 13, 32, 32, 32, 46, 49, 49, 46, 46, 49, 49, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 13, 46, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485418552 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485418552 Building ZINC000485664634 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485664634 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/174 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)cc1NC(=O)c1ccc(Cl)cc1F) `ZINC000485664634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485664634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000485664634 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)cc1NC(=O)c1ccc(Cl)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 16, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 16, 28, 29, 28, 46, 46, 29, 46, 46, 46, 46, 32, 32, 32, 16, 16, 3, 4, 4, 4, 4, 4, 4, 16, 29, 46, 46, 46] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/175 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/175' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)cc1NC(=O)c1ccc(Cl)cc1F) `ZINC000485664634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485664634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000485664634 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)cc1NC(=O)c1ccc(Cl)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 28, 28, 28, 45, 45, 28, 45, 45, 45, 45, 30, 30, 30, 15, 15, 3, 4, 4, 4, 4, 4, 4, 15, 28, 45, 45, 45] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485664634 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634 Building ZINC000485664634 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485664634 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 174) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)cc1NC(=O)c1ccc(Cl)cc1F) `ZINC000485664634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485664634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000485664634 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)cc1NC(=O)c1ccc(Cl)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 16, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 16, 28, 29, 28, 46, 46, 29, 46, 46, 46, 46, 32, 32, 32, 16, 16, 3, 4, 4, 4, 4, 4, 4, 16, 29, 46, 46, 46] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 175) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)cc1NC(=O)c1ccc(Cl)cc1F) `ZINC000485664634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485664634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000485664634 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)cc1NC(=O)c1ccc(Cl)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 28, 28, 28, 45, 45, 28, 45, 45, 45, 45, 30, 30, 30, 15, 15, 3, 4, 4, 4, 4, 4, 4, 15, 28, 45, 45, 45] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485664634 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485664634 Building ZINC000485684809 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485684809 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/176 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)c(OCC)cc1NC(=O)c1ccccc1) `ZINC000485684809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485684809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000485684809 none CCOc1cc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)c(OCC)cc1NC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 12, 5, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 28, 6, 6, 6, 10, 11, 10, 20, 20, 10, 20, 20, 19, 19, 19, 19, 19, 6, 3, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 6, 11, 20, 20, 19, 20, 20] 50 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 14, 15, 16, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/177 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)c(OCC)cc1NC(=O)c1ccccc1) `ZINC000485684809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485684809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000485684809 none CCOc1cc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)c(OCC)cc1NC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 12, 5, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 17, 28, 6, 6, 6, 11, 11, 11, 21, 21, 11, 21, 21, 18, 18, 18, 18, 18, 6, 3, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 6, 11, 21, 21, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485684809 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809 Building ZINC000485684809 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485684809 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 176) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)c(OCC)cc1NC(=O)c1ccccc1) `ZINC000485684809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485684809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000485684809 none CCOc1cc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)c(OCC)cc1NC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 12, 5, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 28, 6, 6, 6, 10, 11, 10, 20, 20, 10, 20, 20, 19, 19, 19, 19, 19, 6, 3, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 6, 11, 20, 20, 19, 20, 20] 50 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 14, 15, 16, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 177) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)c(OCC)cc1NC(=O)c1ccccc1) `ZINC000485684809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485684809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000485684809 none CCOc1cc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)c(OCC)cc1NC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 12, 5, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 17, 28, 6, 6, 6, 11, 11, 11, 21, 21, 11, 21, 21, 18, 18, 18, 18, 18, 6, 3, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 6, 11, 21, 21, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485684809 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485684809 Building ZINC000485702247 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485702247 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/178 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCc1nc(C(=O)OCC)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[nH]1) `ZINC000485702247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485702247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000485702247 none CCCCc1nc(C(=O)OCC)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 11, 12, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 15, 2, 2, 2, 2, 2, 5, 5, 5, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 21, 15, 15, 11, 11, 11, 11, 11, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/179 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCc1nc(C(=O)OCC)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[nH]1) `ZINC000485702247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485702247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000485702247 none CCCCc1nc(C(=O)OCC)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 11, 12, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 15, 2, 2, 2, 2, 2, 5, 5, 5, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 21, 15, 15, 10, 10, 10, 10, 10, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485702247 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247 Building ZINC000485702247 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485702247 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 178) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/178: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCc1nc(C(=O)OCC)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[nH]1) `ZINC000485702247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485702247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000485702247 none CCCCc1nc(C(=O)OCC)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 11, 12, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 15, 2, 2, 2, 2, 2, 5, 5, 5, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 21, 15, 15, 11, 11, 11, 11, 11, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 179) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/179: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCc1nc(C(=O)OCC)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[nH]1) `ZINC000485702247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485702247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000485702247 none CCCCc1nc(C(=O)OCC)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 11, 12, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 15, 2, 2, 2, 2, 2, 5, 5, 5, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 21, 15, 15, 10, 10, 10, 10, 10, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485702247 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485702247 Building ZINC000485806891 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485806891 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/180 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N(CC(=O)Nc1ccccc1F)Cc1ccc(Cl)cc1) `ZINC000485806891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485806891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000485806891 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N(CC(=O)Nc1ccccc1F)Cc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 6, 10, 22, 22, 22, 36, 36, 25, 36, 36, 36, 6, 12, 13, 13, 12, 13, 13, 13, 5, 5, 5, 5, 5, 5, 10, 10, 22, 36, 36, 35, 36, 12, 12, 13, 13, 13, 13] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 192 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/181 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N(CC(=O)Nc1ccccc1F)Cc1ccc(Cl)cc1) `ZINC000485806891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485806891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000485806891 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N(CC(=O)Nc1ccccc1F)Cc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 6, 10, 20, 20, 20, 35, 35, 22, 35, 35, 35, 6, 12, 13, 13, 12, 12, 13, 13, 3, 3, 3, 3, 3, 3, 10, 10, 20, 35, 35, 35, 35, 12, 12, 13, 13, 13, 13] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 193 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485806891 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891 Building ZINC000485806891 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485806891 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 180) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N(CC(=O)Nc1ccccc1F)Cc1ccc(Cl)cc1) `ZINC000485806891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485806891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000485806891 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N(CC(=O)Nc1ccccc1F)Cc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 6, 10, 22, 22, 22, 36, 36, 25, 36, 36, 36, 6, 12, 13, 13, 12, 13, 13, 13, 5, 5, 5, 5, 5, 5, 10, 10, 22, 36, 36, 35, 36, 12, 12, 13, 13, 13, 13] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 192 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 181) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N(CC(=O)Nc1ccccc1F)Cc1ccc(Cl)cc1) `ZINC000485806891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485806891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000485806891 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N(CC(=O)Nc1ccccc1F)Cc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 6, 10, 20, 20, 20, 35, 35, 22, 35, 35, 35, 6, 12, 13, 13, 12, 12, 13, 13, 3, 3, 3, 3, 3, 3, 10, 10, 20, 35, 35, 35, 35, 12, 12, 13, 13, 13, 13] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 193 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485806891 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485806891 Building ZINC000485940964 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485940964 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/182 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n([C@@H](C)C(=O)Nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cccn3C)cc2Cl)n1) `ZINC000485940964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485940964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485940964 none Cc1cc(C)n([C@@H](C)C(=O)Nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cccn3C)cc2Cl)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 7, 5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 39, 21, 39, 39, 21, 21, 12, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 12, 49, 49, 49, 49, 49, 49, 49, 49, 39, 39, 39, 21, 12, 12, 2, 3, 3, 3, 3, 3, 3, 12] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/183 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n([C@@H](C)C(=O)Nc2ccc(NC(=O)[C@]([O-])([SiH3])c3cccn3C)cc2Cl)n1) `ZINC000485940964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485940964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485940964 none Cc1cc(C)n([C@@H](C)C(=O)Nc2ccc(NC(=O)[C@]([O-])([SiH3])c3cccn3C)cc2Cl)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 7, 5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 35, 22, 35, 35, 22, 22, 13, 9, 13, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 13, 13, 13, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35, 35, 22, 13, 13, 2, 4, 4, 4, 4, 4, 4, 13] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485940964 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964 Building ZINC000485940964 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485940964 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 182) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n([C@@H](C)C(=O)Nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cccn3C)cc2Cl)n1) `ZINC000485940964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485940964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485940964 none Cc1cc(C)n([C@@H](C)C(=O)Nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cccn3C)cc2Cl)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 7, 5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 39, 21, 39, 39, 21, 21, 12, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 12, 49, 49, 49, 49, 49, 49, 49, 49, 39, 39, 39, 21, 12, 12, 2, 3, 3, 3, 3, 3, 3, 12] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 183) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n([C@@H](C)C(=O)Nc2ccc(NC(=O)[C@]([O-])([SiH3])c3cccn3C)cc2Cl)n1) `ZINC000485940964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485940964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485940964 none Cc1cc(C)n([C@@H](C)C(=O)Nc2ccc(NC(=O)[C@]([O-])([SiH3])c3cccn3C)cc2Cl)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 7, 5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 35, 22, 35, 35, 22, 22, 13, 9, 13, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 13, 13, 13, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35, 35, 22, 13, 13, 2, 4, 4, 4, 4, 4, 4, 13] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485940964 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940964 Building ZINC000485940965 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485940965 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/184 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n([C@H](C)C(=O)Nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cccn3C)cc2Cl)n1) `ZINC000485940965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485940965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485940965 none Cc1cc(C)n([C@H](C)C(=O)Nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cccn3C)cc2Cl)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 7, 5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 35, 22, 34, 34, 22, 22, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35, 34, 22, 13, 13, 2, 3, 3, 3, 3, 3, 3, 13] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/185 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n([C@H](C)C(=O)Nc2ccc(NC(=O)[C@]([O-])([SiH3])c3cccn3C)cc2Cl)n1) `ZINC000485940965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485940965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485940965 none Cc1cc(C)n([C@H](C)C(=O)Nc2ccc(NC(=O)[C@]([O-])([SiH3])c3cccn3C)cc2Cl)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 7, 5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 39, 21, 39, 39, 21, 21, 12, 9, 12, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 12, 12, 12, 48, 48, 48, 48, 48, 48, 48, 48, 39, 39, 39, 21, 12, 12, 2, 4, 4, 4, 4, 4, 4, 12] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485940965 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965 Building ZINC000485940965 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485940965 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 184) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n([C@H](C)C(=O)Nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cccn3C)cc2Cl)n1) `ZINC000485940965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485940965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485940965 none Cc1cc(C)n([C@H](C)C(=O)Nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cccn3C)cc2Cl)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 7, 5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 35, 22, 34, 34, 22, 22, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35, 34, 22, 13, 13, 2, 3, 3, 3, 3, 3, 3, 13] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 185) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n([C@H](C)C(=O)Nc2ccc(NC(=O)[C@]([O-])([SiH3])c3cccn3C)cc2Cl)n1) `ZINC000485940965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485940965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485940965 none Cc1cc(C)n([C@H](C)C(=O)Nc2ccc(NC(=O)[C@]([O-])([SiH3])c3cccn3C)cc2Cl)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 7, 5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 39, 21, 39, 39, 21, 21, 12, 9, 12, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 12, 12, 12, 48, 48, 48, 48, 48, 48, 48, 48, 39, 39, 39, 21, 12, 12, 2, 4, 4, 4, 4, 4, 4, 12] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000485940965 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000485940965 Building ZINC000486195395 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486195395 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/186 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cccn2C)c2ccccc2)cc1Br) `ZINC000486195395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486195395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000486195395 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cccn2C)c2ccccc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 35, 12, 35, 35, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 6, 12, 12, 6, 12, 12, 35, 35, 35, 47, 47, 47, 35, 35, 3, 3, 3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 35] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 179 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/187 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cccn2C)c2ccccc2)cc1Br) `ZINC000486195395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486195395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000486195395 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cccn2C)c2ccccc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 13, 11, 33, 33, 6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 6, 10, 10, 6, 10, 10, 33, 33, 33, 47, 47, 47, 33, 33, 3, 4, 4, 4, 4, 4, 4, 10, 10, 6, 10, 10, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 158 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486195395 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395 Building ZINC000486195395 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486195395 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 186) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/186: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cccn2C)c2ccccc2)cc1Br) `ZINC000486195395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486195395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000486195395 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cccn2C)c2ccccc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 35, 12, 35, 35, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 6, 12, 12, 6, 12, 12, 35, 35, 35, 47, 47, 47, 35, 35, 3, 3, 3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 35] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 179 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 187) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cccn2C)c2ccccc2)cc1Br) `ZINC000486195395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486195395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000486195395 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cccn2C)c2ccccc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 13, 11, 33, 33, 6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 6, 10, 10, 6, 10, 10, 33, 33, 33, 47, 47, 47, 33, 33, 3, 4, 4, 4, 4, 4, 4, 10, 10, 6, 10, 10, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 158 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486195395 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195395 Building ZINC000486195397 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486195397 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/188 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cccn2C)c2ccccc2)cc1Br) `ZINC000486195397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486195397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000486195397 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cccn2C)c2ccccc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 22, 13, 33, 33, 6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 6, 10, 10, 6, 10, 10, 33, 33, 33, 47, 47, 47, 33, 33, 3, 4, 4, 4, 4, 4, 4, 10, 10, 6, 10, 10, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 160 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/189 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cccn2C)c2ccccc2)cc1Br) `ZINC000486195397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486195397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000486195397 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cccn2C)c2ccccc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 30, 12, 34, 34, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 6, 12, 12, 7, 12, 12, 34, 34, 34, 46, 46, 46, 34, 34, 3, 3, 3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 34] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 175 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486195397 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397 Building ZINC000486195397 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486195397 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 188) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cccn2C)c2ccccc2)cc1Br) `ZINC000486195397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486195397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000486195397 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cccn2C)c2ccccc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 22, 13, 33, 33, 6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 6, 10, 10, 6, 10, 10, 33, 33, 33, 47, 47, 47, 33, 33, 3, 4, 4, 4, 4, 4, 4, 10, 10, 6, 10, 10, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 160 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 189) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cccn2C)c2ccccc2)cc1Br) `ZINC000486195397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486195397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000486195397 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cccn2C)c2ccccc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 30, 12, 34, 34, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 6, 12, 12, 7, 12, 12, 34, 34, 34, 46, 46, 46, 34, 34, 3, 3, 3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 34] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 175 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486195397 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486195397 Building ZINC000486199995 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486199995 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/190 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1nc2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2s1) `ZINC000486199995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486199995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000486199995 none CC(=O)Nc1nc2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 14, 14, 14, 14, 14, 14, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 14, 14, 14, 31, 31, 31, 31, 14, 14, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 93 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/191 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2s1) `ZINC000486199995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486199995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000486199995 none CC(=O)Nc1nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 12, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 12, 12, 12, 21, 21, 21, 21, 12, 12, 2, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486199995 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995 Building ZINC000486199995 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486199995 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 190) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1nc2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2s1) `ZINC000486199995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486199995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000486199995 none CC(=O)Nc1nc2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 14, 14, 14, 14, 14, 14, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 14, 14, 14, 31, 31, 31, 31, 14, 14, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 93 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 191) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2s1) `ZINC000486199995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486199995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000486199995 none CC(=O)Nc1nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 12, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 12, 12, 12, 21, 21, 21, 21, 12, 12, 2, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486199995 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486199995 Building ZINC000486235204 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486235204 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/192 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CC(=O)Nc1ccc(Cl)cc1C(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000486235204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486235204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000486235204 none CC(C)N(CC(=O)Nc1ccc(Cl)cc1C(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 12, 4, 8, 17, 34, 34, 34, 43, 43, 34, 34, 43, 43, 43, 43, 43, 43, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 17, 17, 34, 43, 43, 43, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/193 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/193' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CC(=O)Nc1ccc(Cl)cc1C(F)(F)F)C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000486235204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486235204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000486235204 none CC(C)N(CC(=O)Nc1ccc(Cl)cc1C(F)(F)F)C(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 10, 4, 8, 17, 31, 31, 31, 41, 41, 31, 32, 41, 41, 41, 41, 41, 41, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 17, 17, 31, 41, 41, 41, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486235204 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204 Building ZINC000486235204 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486235204 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 192) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CC(=O)Nc1ccc(Cl)cc1C(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000486235204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486235204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000486235204 none CC(C)N(CC(=O)Nc1ccc(Cl)cc1C(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 12, 4, 8, 17, 34, 34, 34, 43, 43, 34, 34, 43, 43, 43, 43, 43, 43, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 17, 17, 34, 43, 43, 43, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 193) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CC(=O)Nc1ccc(Cl)cc1C(F)(F)F)C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000486235204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486235204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000486235204 none CC(C)N(CC(=O)Nc1ccc(Cl)cc1C(F)(F)F)C(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 10, 4, 8, 17, 31, 31, 31, 41, 41, 31, 32, 41, 41, 41, 41, 41, 41, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 17, 17, 31, 41, 41, 41, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486235204 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486235204 Building ZINC000486274496 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486274496 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/194 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(C)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1Br) `ZINC000486274496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486274496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000486274496 none COC(=O)c1c(C)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 10, 28, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 10, 10, 10, 10, 28, 28, 28, 10, 10, 10, 3, 6, 7, 7, 6, 7, 7, 6, 10, 10] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/195 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/195' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(C)c(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1Br) `ZINC000486274496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486274496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000486274496 none COC(=O)c1c(C)c(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 10, 28, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 10, 10, 10, 10, 28, 28, 28, 10, 10, 10, 3, 6, 7, 7, 6, 7, 7, 6, 10, 10] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486274496 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496 Building ZINC000486274496 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486274496 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 194) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(C)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1Br) `ZINC000486274496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486274496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000486274496 none COC(=O)c1c(C)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 10, 28, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 10, 10, 10, 10, 28, 28, 28, 10, 10, 10, 3, 6, 7, 7, 6, 7, 7, 6, 10, 10] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 195) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(C)c(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1Br) `ZINC000486274496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486274496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000486274496 none COC(=O)c1c(C)c(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 10, 28, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 10, 10, 10, 10, 28, 28, 28, 10, 10, 10, 3, 6, 7, 7, 6, 7, 7, 6, 10, 10] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486274496 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486274496 Building ZINC000486507736 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486507736 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/196 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC000486507736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486507736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000486507736 none COC(=O)CCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 30, 48, 18, 8, 6, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 48, 48, 48, 30, 30, 18, 18, 8, 8, 2, 2, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 43, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/197 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/197' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC000486507736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486507736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000486507736 none COC(=O)CCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 32, 49, 20, 9, 6, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 49, 49, 49, 32, 32, 20, 20, 9, 9, 2, 2, 1, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 43, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486507736 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736 Building ZINC000486507736 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486507736 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 196) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC000486507736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486507736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000486507736 none COC(=O)CCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 30, 48, 18, 8, 6, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 48, 48, 48, 30, 30, 18, 18, 8, 8, 2, 2, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 43, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 197) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC000486507736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486507736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000486507736 none COC(=O)CCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 32, 49, 20, 9, 6, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 49, 49, 49, 32, 32, 20, 20, 9, 9, 2, 2, 1, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 43, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486507736 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486507736 Building ZINC000486651176 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486651176 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/198 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(Sc2ccc(Cl)cn2)c(NC(=O)[C@]([O-])([SiH3])c2cccn2C)c1) `ZINC000486651176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486651176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000486651176 none COC(=O)c1ccc(Sc2ccc(Cl)cn2)c(NC(=O)[C@]([O-])([SiH3])c2cccn2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 16, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 10, 19, 10, 10, 10, 10, 10, 32, 35, 35, 35, 35, 35, 35, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 10, 19, 19, 19, 10, 10, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/199 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(Sc2ccc(Cl)cn2)c(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)c1) `ZINC000486651176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486651176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000486651176 none COC(=O)c1ccc(Sc2ccc(Cl)cn2)c(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 16, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 9, 19, 9, 9, 9, 9, 9, 32, 36, 36, 36, 36, 36, 36, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 9, 19, 19, 19, 9, 9, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 9] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486651176 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176 Building ZINC000486651176 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486651176 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 198) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(Sc2ccc(Cl)cn2)c(NC(=O)[C@]([O-])([SiH3])c2cccn2C)c1) `ZINC000486651176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486651176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000486651176 none COC(=O)c1ccc(Sc2ccc(Cl)cn2)c(NC(=O)[C@]([O-])([SiH3])c2cccn2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 16, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 10, 19, 10, 10, 10, 10, 10, 32, 35, 35, 35, 35, 35, 35, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 10, 19, 19, 19, 10, 10, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 199) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(Sc2ccc(Cl)cn2)c(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)c1) `ZINC000486651176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486651176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000486651176 none COC(=O)c1ccc(Sc2ccc(Cl)cn2)c(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 16, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 9, 19, 9, 9, 9, 9, 9, 32, 36, 36, 36, 36, 36, 36, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 9, 19, 19, 19, 9, 9, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 9] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486651176 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486651176 Building ZINC000486799975 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486799975 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/200 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cc(OC)c1OC) `ZINC000486799975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486799975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000486799975 none COc1cc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cc(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 23, 23, 23, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 23, 23, 23, 40, 8, 18, 45, 39, 39, 39, 23, 4, 3, 3, 3, 3, 23, 40, 40, 40, 45, 45, 45] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 206 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/201 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cc(OC)c1OC) `ZINC000486799975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486799975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000486799975 none COc1cc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cc(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 19, 19, 19, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 19, 19, 19, 36, 11, 15, 45, 35, 35, 35, 19, 4, 3, 3, 3, 3, 19, 36, 36, 36, 45, 45, 45] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 171 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486799975 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975 Building ZINC000486799975 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486799975 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 200) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/200: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cc(OC)c1OC) `ZINC000486799975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486799975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000486799975 none COc1cc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cc(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 23, 23, 23, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 23, 23, 23, 40, 8, 18, 45, 39, 39, 39, 23, 4, 3, 3, 3, 3, 23, 40, 40, 40, 45, 45, 45] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 206 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 201) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/201: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cc(OC)c1OC) `ZINC000486799975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486799975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000486799975 none COc1cc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cc(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 19, 19, 19, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 19, 19, 19, 36, 11, 15, 45, 35, 35, 35, 19, 4, 3, 3, 3, 3, 19, 36, 36, 36, 45, 45, 45] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 171 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486799975 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799975 Building ZINC000486799976 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486799976 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/202 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cc(OC)c1OC) `ZINC000486799976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486799976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000486799976 none COc1cc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cc(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 18, 18, 18, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 18, 18, 18, 34, 16, 18, 45, 35, 35, 35, 18, 4, 3, 3, 3, 3, 18, 34, 34, 34, 45, 45, 45] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 154 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/203 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cc(OC)c1OC) `ZINC000486799976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486799976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000486799976 none COc1cc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cc(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 23, 23, 23, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 8, 8, 8, 23, 23, 23, 39, 18, 23, 45, 40, 40, 40, 23, 4, 3, 3, 3, 3, 23, 39, 39, 39, 45, 45, 45] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 171 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486799976 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976 Building ZINC000486799976 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486799976 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 202) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/202: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cc(OC)c1OC) `ZINC000486799976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486799976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000486799976 none COc1cc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cc(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 18, 18, 18, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 18, 18, 18, 34, 16, 18, 45, 35, 35, 35, 18, 4, 3, 3, 3, 3, 18, 34, 34, 34, 45, 45, 45] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 154 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 203) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/203: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cc(OC)c1OC) `ZINC000486799976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486799976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000486799976 none COc1cc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cc(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 23, 23, 23, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 8, 8, 8, 23, 23, 23, 39, 18, 23, 45, 40, 40, 40, 23, 4, 3, 3, 3, 3, 23, 39, 39, 39, 45, 45, 45] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 171 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486799976 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486799976 Building ZINC000486889668 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486889668 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/204 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2cccc(C(F)(F)F)c2)CCOCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000486889668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486889668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486889668 none O=C(NC1(c2cccc(C(F)(F)F)c2)CCOCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 9, 21, 21, 16, 21, 21, 21, 21, 21, 21, 9, 9, 9, 9, 9, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 3, 21, 21, 9, 21, 9, 9, 9, 9, 9, 9, 9, 9, 6, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/205 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2cccc(C(F)(F)F)c2)CCOCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000486889668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486889668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486889668 none O=C(NC1(c2cccc(C(F)(F)F)c2)CCOCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 9, 22, 22, 17, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 1, 1, 1, 7, 7, 7, 7, 9, 9, 7, 9, 9, 7, 4, 22, 22, 17, 22, 9, 9, 9, 9, 9, 9, 9, 9, 7, 9, 9, 9, 9, 9, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486889668 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668 Building ZINC000486889668 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486889668 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 204) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/204: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2cccc(C(F)(F)F)c2)CCOCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000486889668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486889668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486889668 none O=C(NC1(c2cccc(C(F)(F)F)c2)CCOCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 9, 21, 21, 16, 21, 21, 21, 21, 21, 21, 9, 9, 9, 9, 9, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 3, 21, 21, 9, 21, 9, 9, 9, 9, 9, 9, 9, 9, 6, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 205) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/205: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2cccc(C(F)(F)F)c2)CCOCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000486889668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486889668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486889668 none O=C(NC1(c2cccc(C(F)(F)F)c2)CCOCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 9, 22, 22, 17, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 1, 1, 1, 7, 7, 7, 7, 9, 9, 7, 9, 9, 7, 4, 22, 22, 17, 22, 9, 9, 9, 9, 9, 9, 9, 9, 7, 9, 9, 9, 9, 9, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486889668 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486889668 Building ZINC000486887611 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000486887611 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/206 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1) `ZINC000486887611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486887611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887611 none CC(C)[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 24, 11, 17, 7, 5, 7, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 17, 20, 20, 20, 35, 35, 48, 48, 40, 41, 48, 48, 24, 24, 24, 24, 24, 24, 24, 11, 11, 7, 7, 7, 4, 4, 4, 4, 20, 48, 48, 48, 48] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/207 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1) `ZINC000486887611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486887611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887611 none CC(C)[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 17, 28, 9, 17, 6, 5, 6, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 17, 23, 23, 23, 33, 33, 50, 50, 33, 33, 50, 50, 28, 28, 28, 28, 28, 28, 28, 9, 9, 6, 6, 6, 2, 2, 2, 2, 23, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/208 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/208' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000486887611.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000486887611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887611 none CC(C)[C@@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 17, 3, 6, 6, 13, 15, 15, 26, 26, 37, 37, 50, 50, 39, 39, 50, 50, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 13, 13, 15, 15, 15, 50, 50, 50, 50, 3, 3, 3, 3, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/209 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/209' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000486887611.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000486887611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887611 none CC(C)[C@@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 17, 4, 8, 8, 13, 15, 15, 24, 24, 36, 36, 44, 44, 36, 37, 44, 44, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 13, 13, 15, 15, 15, 44, 44, 44, 44, 4, 3, 3, 3, 3] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486887611 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 Building ZINC000486887611 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000486887611 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 206) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/206: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1) `ZINC000486887611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486887611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887611 none CC(C)[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 24, 11, 17, 7, 5, 7, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 17, 20, 20, 20, 35, 35, 48, 48, 40, 41, 48, 48, 24, 24, 24, 24, 24, 24, 24, 11, 11, 7, 7, 7, 4, 4, 4, 4, 20, 48, 48, 48, 48] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 207) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/207: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1) `ZINC000486887611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486887611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887611 none CC(C)[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 17, 28, 9, 17, 6, 5, 6, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 17, 23, 23, 23, 33, 33, 50, 50, 33, 33, 50, 50, 28, 28, 28, 28, 28, 28, 28, 9, 9, 6, 6, 6, 2, 2, 2, 2, 23, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 208) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/208: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000486887611.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000486887611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887611 none CC(C)[C@@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 17, 3, 6, 6, 13, 15, 15, 26, 26, 37, 37, 50, 50, 39, 39, 50, 50, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 13, 13, 15, 15, 15, 50, 50, 50, 50, 3, 3, 3, 3, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 209) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/209: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000486887611.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000486887611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887611 none CC(C)[C@@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 17, 4, 8, 8, 13, 15, 15, 24, 24, 36, 36, 44, 44, 36, 37, 44, 44, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 13, 13, 15, 15, 15, 44, 44, 44, 44, 4, 3, 3, 3, 3] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486887611 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 Building ZINC000486887611 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000486887611 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 206) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/206: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1) `ZINC000486887611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486887611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887611 none CC(C)[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 24, 11, 17, 7, 5, 7, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 17, 20, 20, 20, 35, 35, 48, 48, 40, 41, 48, 48, 24, 24, 24, 24, 24, 24, 24, 11, 11, 7, 7, 7, 4, 4, 4, 4, 20, 48, 48, 48, 48] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 207) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/207: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1) `ZINC000486887611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486887611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887611 none CC(C)[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 17, 28, 9, 17, 6, 5, 6, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 17, 23, 23, 23, 33, 33, 50, 50, 33, 33, 50, 50, 28, 28, 28, 28, 28, 28, 28, 9, 9, 6, 6, 6, 2, 2, 2, 2, 23, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 208) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/208: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000486887611.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000486887611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887611 none CC(C)[C@@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 17, 3, 6, 6, 13, 15, 15, 26, 26, 37, 37, 50, 50, 39, 39, 50, 50, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 13, 13, 15, 15, 15, 50, 50, 50, 50, 3, 3, 3, 3, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 209) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/209: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000486887611.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000486887611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887611 none CC(C)[C@@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 17, 4, 8, 8, 13, 15, 15, 24, 24, 36, 36, 44, 44, 36, 37, 44, 44, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 13, 13, 15, 15, 15, 44, 44, 44, 44, 4, 3, 3, 3, 3] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486887611 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 Building ZINC000486887611 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000486887611 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 206) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/206: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1) `ZINC000486887611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486887611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887611 none CC(C)[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 24, 11, 17, 7, 5, 7, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 17, 20, 20, 20, 35, 35, 48, 48, 40, 41, 48, 48, 24, 24, 24, 24, 24, 24, 24, 11, 11, 7, 7, 7, 4, 4, 4, 4, 20, 48, 48, 48, 48] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 207) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/207: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1) `ZINC000486887611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486887611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887611 none CC(C)[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 17, 28, 9, 17, 6, 5, 6, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 17, 23, 23, 23, 33, 33, 50, 50, 33, 33, 50, 50, 28, 28, 28, 28, 28, 28, 28, 9, 9, 6, 6, 6, 2, 2, 2, 2, 23, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 208) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/208: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000486887611.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000486887611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887611 none CC(C)[C@@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 17, 3, 6, 6, 13, 15, 15, 26, 26, 37, 37, 50, 50, 39, 39, 50, 50, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 13, 13, 15, 15, 15, 50, 50, 50, 50, 3, 3, 3, 3, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 209) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/209: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000486887611.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000486887611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887611 none CC(C)[C@@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 17, 4, 8, 8, 13, 15, 15, 24, 24, 36, 36, 44, 44, 36, 37, 44, 44, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 13, 13, 15, 15, 15, 44, 44, 44, 44, 4, 3, 3, 3, 3] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486887611 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887611 Building ZINC000486887612 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000486887612 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/210 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1) `ZINC000486887612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486887612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887612 none CC(C)[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 18, 28, 10, 18, 7, 5, 7, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 23, 23, 23, 32, 32, 50, 50, 32, 42, 50, 50, 28, 28, 28, 28, 28, 28, 28, 10, 10, 7, 7, 7, 2, 2, 2, 2, 23, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/211 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1) `ZINC000486887612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486887612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887612 none CC(C)[C@H](CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 24, 11, 17, 7, 5, 7, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 20, 20, 20, 35, 35, 49, 49, 35, 35, 49, 49, 24, 24, 24, 24, 24, 24, 24, 11, 11, 7, 7, 7, 3, 3, 3, 3, 20, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 223 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/212 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/212' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000486887612.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000486887612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887612 none CC(C)[C@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 16, 4, 8, 8, 13, 15, 15, 24, 24, 37, 37, 44, 44, 37, 38, 44, 44, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 13, 13, 15, 15, 15, 44, 44, 44, 44, 4, 3, 3, 3, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/213 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/213' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000486887612.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000486887612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887612 none CC(C)[C@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 17, 3, 6, 6, 13, 15, 15, 25, 25, 36, 36, 49, 49, 38, 38, 49, 49, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 13, 13, 15, 15, 15, 49, 49, 49, 49, 3, 3, 3, 3, 3] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486887612 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 Building ZINC000486887612 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000486887612 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 210) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/210: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1) `ZINC000486887612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486887612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887612 none CC(C)[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 18, 28, 10, 18, 7, 5, 7, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 23, 23, 23, 32, 32, 50, 50, 32, 42, 50, 50, 28, 28, 28, 28, 28, 28, 28, 10, 10, 7, 7, 7, 2, 2, 2, 2, 23, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 211) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/211: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1) `ZINC000486887612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486887612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887612 none CC(C)[C@H](CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 24, 11, 17, 7, 5, 7, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 20, 20, 20, 35, 35, 49, 49, 35, 35, 49, 49, 24, 24, 24, 24, 24, 24, 24, 11, 11, 7, 7, 7, 3, 3, 3, 3, 20, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 223 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 212) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/212: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000486887612.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000486887612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887612 none CC(C)[C@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 16, 4, 8, 8, 13, 15, 15, 24, 24, 37, 37, 44, 44, 37, 38, 44, 44, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 13, 13, 15, 15, 15, 44, 44, 44, 44, 4, 3, 3, 3, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 213) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/213: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000486887612.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000486887612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887612 none CC(C)[C@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 17, 3, 6, 6, 13, 15, 15, 25, 25, 36, 36, 49, 49, 38, 38, 49, 49, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 13, 13, 15, 15, 15, 49, 49, 49, 49, 3, 3, 3, 3, 3] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486887612 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 Building ZINC000486887612 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000486887612 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 210) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/210: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1) `ZINC000486887612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486887612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887612 none CC(C)[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 18, 28, 10, 18, 7, 5, 7, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 23, 23, 23, 32, 32, 50, 50, 32, 42, 50, 50, 28, 28, 28, 28, 28, 28, 28, 10, 10, 7, 7, 7, 2, 2, 2, 2, 23, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 211) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/211: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1) `ZINC000486887612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486887612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887612 none CC(C)[C@H](CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 24, 11, 17, 7, 5, 7, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 20, 20, 20, 35, 35, 49, 49, 35, 35, 49, 49, 24, 24, 24, 24, 24, 24, 24, 11, 11, 7, 7, 7, 3, 3, 3, 3, 20, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 223 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 212) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/212: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000486887612.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000486887612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887612 none CC(C)[C@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 16, 4, 8, 8, 13, 15, 15, 24, 24, 37, 37, 44, 44, 37, 38, 44, 44, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 13, 13, 15, 15, 15, 44, 44, 44, 44, 4, 3, 3, 3, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 213) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/213: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000486887612.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000486887612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887612 none CC(C)[C@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 17, 3, 6, 6, 13, 15, 15, 25, 25, 36, 36, 49, 49, 38, 38, 49, 49, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 13, 13, 15, 15, 15, 49, 49, 49, 49, 3, 3, 3, 3, 3] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486887612 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 Building ZINC000486887612 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000486887612 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 210) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/210: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1) `ZINC000486887612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486887612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887612 none CC(C)[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 18, 28, 10, 18, 7, 5, 7, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 23, 23, 23, 32, 32, 50, 50, 32, 42, 50, 50, 28, 28, 28, 28, 28, 28, 28, 10, 10, 7, 7, 7, 2, 2, 2, 2, 23, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 211) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/211: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1) `ZINC000486887612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486887612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887612 none CC(C)[C@H](CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)NC(=O)C(=O)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 24, 11, 17, 7, 5, 7, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 20, 20, 20, 35, 35, 49, 49, 35, 35, 49, 49, 24, 24, 24, 24, 24, 24, 24, 11, 11, 7, 7, 7, 3, 3, 3, 3, 20, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 223 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 212) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/212: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000486887612.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000486887612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887612 none CC(C)[C@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 16, 4, 8, 8, 13, 15, 15, 24, 24, 37, 37, 44, 44, 37, 38, 44, 44, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 13, 13, 15, 15, 15, 44, 44, 44, 44, 4, 3, 3, 3, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 213) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/213: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000486887612.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000486887612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000486887612 none CC(C)[C@H](CN(C)C(=O)C(=O)c1ccc(Cl)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 17, 3, 6, 6, 13, 15, 15, 25, 25, 36, 36, 49, 49, 38, 38, 49, 49, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 13, 13, 15, 15, 15, 49, 49, 49, 49, 3, 3, 3, 3, 3] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000486887612 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000486887612 Building ZINC000760620172 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760620172 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/214 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CCN3CCCC3=O)c3ccccc32)cc1Cl) `ZINC000760620172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760620172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000760620172 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CCN3CCCC3=O)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 2, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 13, 18, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 3, 3, 3, 8, 8, 8, 3, 3, 4, 4, 13, 13, 18, 18, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4, 3] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/215 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](CCN3CCCC3=O)c3ccccc32)cc1Cl) `ZINC000760620172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760620172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000760620172 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](CCN3CCCC3=O)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 13, 20, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 2, 2, 2, 5, 5, 5, 2, 2, 6, 6, 13, 13, 20, 20, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760620172 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172 Building ZINC000760620172 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760620172 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 214) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/214: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CCN3CCCC3=O)c3ccccc32)cc1Cl) `ZINC000760620172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760620172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000760620172 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CCN3CCCC3=O)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 2, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 13, 18, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 3, 3, 3, 8, 8, 8, 3, 3, 4, 4, 13, 13, 18, 18, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4, 3] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 215) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/215: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](CCN3CCCC3=O)c3ccccc32)cc1Cl) `ZINC000760620172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760620172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000760620172 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](CCN3CCCC3=O)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 13, 20, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 2, 2, 2, 5, 5, 5, 2, 2, 6, 6, 13, 13, 20, 20, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760620172 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620172 Building ZINC000760620174 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760620174 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/216 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](CCN3CCCC3=O)c3ccccc32)cc1Cl) `ZINC000760620174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760620174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000760620174 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](CCN3CCCC3=O)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 12, 18, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 2, 2, 2, 5, 5, 5, 2, 2, 6, 6, 12, 12, 18, 18, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/217 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](CCN3CCCC3=O)c3ccccc32)cc1Cl) `ZINC000760620174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760620174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000760620174 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](CCN3CCCC3=O)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 2, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 12, 16, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 2, 2, 2, 6, 6, 6, 2, 2, 4, 4, 12, 12, 16, 16, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760620174 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174 Building ZINC000760620174 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760620174 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 216) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/216: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](CCN3CCCC3=O)c3ccccc32)cc1Cl) `ZINC000760620174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760620174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000760620174 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](CCN3CCCC3=O)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 12, 18, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 2, 2, 2, 5, 5, 5, 2, 2, 6, 6, 12, 12, 18, 18, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 217) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/217: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](CCN3CCCC3=O)c3ccccc32)cc1Cl) `ZINC000760620174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760620174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000760620174 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](CCN3CCCC3=O)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 2, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 12, 16, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 2, 2, 2, 6, 6, 6, 2, 2, 4, 4, 12, 12, 16, 16, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760620174 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760620174 Building ZINC000488132525 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488132525 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/218 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488132525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132525 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 26, 26, 19, 26, 26, 26, 10, 4, 4, 4, 9, 9, 9, 4, 4, 2, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/219 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488132525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132525 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 26, 26, 18, 26, 26, 26, 10, 4, 4, 4, 8, 8, 8, 4, 4, 2, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/220 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/220' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132525.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488132525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132525 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 26, 26, 19, 26, 26, 26, 10, 4, 4, 4, 9, 9, 9, 4, 4, 2, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/221 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/221' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132525.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488132525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132525 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 26, 26, 18, 26, 26, 26, 10, 4, 4, 4, 8, 8, 8, 4, 4, 2, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488132525 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 Building ZINC000488132525 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488132525 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 218) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/218: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488132525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132525 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 26, 26, 19, 26, 26, 26, 10, 4, 4, 4, 9, 9, 9, 4, 4, 2, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 219) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/219: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488132525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132525 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 26, 26, 18, 26, 26, 26, 10, 4, 4, 4, 8, 8, 8, 4, 4, 2, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 220) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/220: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132525.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488132525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132525 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 26, 26, 19, 26, 26, 26, 10, 4, 4, 4, 9, 9, 9, 4, 4, 2, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 221) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/221: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132525.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488132525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132525 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 26, 26, 18, 26, 26, 26, 10, 4, 4, 4, 8, 8, 8, 4, 4, 2, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488132525 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 Building ZINC000488132525 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488132525 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 218) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/218: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488132525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132525 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 26, 26, 19, 26, 26, 26, 10, 4, 4, 4, 9, 9, 9, 4, 4, 2, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 219) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/219: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488132525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132525 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 26, 26, 18, 26, 26, 26, 10, 4, 4, 4, 8, 8, 8, 4, 4, 2, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 220) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/220: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132525.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488132525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132525 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 26, 26, 19, 26, 26, 26, 10, 4, 4, 4, 9, 9, 9, 4, 4, 2, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 221) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/221: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132525.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488132525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132525 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 26, 26, 18, 26, 26, 26, 10, 4, 4, 4, 8, 8, 8, 4, 4, 2, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488132525 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 Building ZINC000488132525 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488132525 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 218) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/218: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488132525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132525 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 26, 26, 19, 26, 26, 26, 10, 4, 4, 4, 9, 9, 9, 4, 4, 2, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 219) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/219: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488132525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132525 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 26, 26, 18, 26, 26, 26, 10, 4, 4, 4, 8, 8, 8, 4, 4, 2, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 220) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/220: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132525.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488132525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132525 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 26, 26, 19, 26, 26, 26, 10, 4, 4, 4, 9, 9, 9, 4, 4, 2, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 221) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/221: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132525.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488132525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132525 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 26, 26, 18, 26, 26, 26, 10, 4, 4, 4, 8, 8, 8, 4, 4, 2, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488132525 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132525 Building ZINC000488132526 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488132526 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/222 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488132526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132526 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 26, 26, 18, 26, 26, 26, 9, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 9, 9, 26, 26, 18, 26, 9, 9, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/223 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488132526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132526 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 10, 4, 4, 4, 9, 9, 9, 4, 4, 2, 10, 10, 10, 10, 25, 25, 25, 25, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/224 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/224' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132526.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488132526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132526 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 26, 26, 18, 26, 26, 26, 9, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 9, 9, 26, 26, 18, 26, 9, 9, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/225 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/225' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132526.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488132526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132526 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 10, 4, 4, 4, 9, 9, 9, 4, 4, 2, 10, 10, 10, 10, 25, 25, 25, 25, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488132526 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 Building ZINC000488132526 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488132526 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 222) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/222: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488132526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132526 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 26, 26, 18, 26, 26, 26, 9, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 9, 9, 26, 26, 18, 26, 9, 9, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 223) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/223: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488132526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132526 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 10, 4, 4, 4, 9, 9, 9, 4, 4, 2, 10, 10, 10, 10, 25, 25, 25, 25, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 224) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/224: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132526.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488132526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132526 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 26, 26, 18, 26, 26, 26, 9, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 9, 9, 26, 26, 18, 26, 9, 9, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 225) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132526.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488132526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132526 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 10, 4, 4, 4, 9, 9, 9, 4, 4, 2, 10, 10, 10, 10, 25, 25, 25, 25, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488132526 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 Building ZINC000488132526 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488132526 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 222) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/222: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488132526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132526 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 26, 26, 18, 26, 26, 26, 9, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 9, 9, 26, 26, 18, 26, 9, 9, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 223) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/223: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488132526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132526 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 10, 4, 4, 4, 9, 9, 9, 4, 4, 2, 10, 10, 10, 10, 25, 25, 25, 25, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 224) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/224: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132526.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488132526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132526 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 26, 26, 18, 26, 26, 26, 9, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 9, 9, 26, 26, 18, 26, 9, 9, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 225) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132526.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488132526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132526 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 10, 4, 4, 4, 9, 9, 9, 4, 4, 2, 10, 10, 10, 10, 25, 25, 25, 25, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488132526 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 Building ZINC000488132526 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488132526 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 222) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/222: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488132526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132526 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 26, 26, 18, 26, 26, 26, 9, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 9, 9, 26, 26, 18, 26, 9, 9, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 223) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/223: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488132526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132526 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 10, 4, 4, 4, 9, 9, 9, 4, 4, 2, 10, 10, 10, 10, 25, 25, 25, 25, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 224) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/224: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132526.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488132526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132526 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 26, 26, 18, 26, 26, 26, 9, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 9, 9, 26, 26, 18, 26, 9, 9, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 225) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl) `ZINC000488132526.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488132526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488132526 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3cccc(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 10, 4, 4, 4, 9, 9, 9, 4, 4, 2, 10, 10, 10, 10, 25, 25, 25, 25, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488132526 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488132526 Building ZINC000488238677 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488238677 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/226 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC2(CCCC2)C1) `ZINC000488238677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488238677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000488238677 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC2(CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 19, 19, 3, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 2, 3, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 19, 19, 3, 19, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 61 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/227 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC2(CCCC2)C1) `ZINC000488238677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488238677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000488238677 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC2(CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488238677 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677 Building ZINC000488238677 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488238677 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 226) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC2(CCCC2)C1) `ZINC000488238677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488238677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000488238677 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC2(CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 19, 19, 3, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 2, 3, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 19, 19, 3, 19, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 61 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 227) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC2(CCCC2)C1) `ZINC000488238677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488238677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000488238677 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC2(CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488238677 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488238677 Building ZINC000488345034 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488345034 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/228 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(c1ccccc1)S(=O)(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)c1) `ZINC000488345034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488345034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000488345034 none CCCCN(c1ccccc1)S(=O)(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 47, 37, 27, 37, 44, 44, 40, 44, 44, 9, 27, 27, 9, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 49, 49, 49, 49, 49, 49, 49, 47, 47, 44, 44, 40, 44, 44, 2, 9, 9, 2, 2, 2, 2, 2, 2, 2, 9] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/229 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(c1ccccc1)S(=O)(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)c1) `ZINC000488345034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488345034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000488345034 none CCCCN(c1ccccc1)S(=O)(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 47, 37, 27, 37, 44, 44, 42, 44, 44, 10, 27, 27, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 49, 49, 49, 49, 49, 49, 49, 47, 47, 44, 44, 42, 44, 44, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 10] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488345034 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034 Building ZINC000488345034 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488345034 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 228) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(c1ccccc1)S(=O)(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)c1) `ZINC000488345034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488345034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000488345034 none CCCCN(c1ccccc1)S(=O)(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 47, 37, 27, 37, 44, 44, 40, 44, 44, 9, 27, 27, 9, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 49, 49, 49, 49, 49, 49, 49, 47, 47, 44, 44, 40, 44, 44, 2, 9, 9, 2, 2, 2, 2, 2, 2, 2, 9] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 229) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/229: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(c1ccccc1)S(=O)(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)c1) `ZINC000488345034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488345034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000488345034 none CCCCN(c1ccccc1)S(=O)(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 47, 37, 27, 37, 44, 44, 42, 44, 44, 10, 27, 27, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 49, 49, 49, 49, 49, 49, 49, 47, 47, 44, 44, 42, 44, 44, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 10] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488345034 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488345034 Building ZINC000488376286 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488376286 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/230 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCN(Cc2ccsc2)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1OC) `ZINC000488376286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488376286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000488376286 none COc1ccc(CCN(Cc2ccsc2)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 14, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 8, 8, 8, 4, 4, 3, 2, 3, 3, 6, 6, 6, 6, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 15, 15, 15, 15, 8, 8, 4, 4, 4, 4, 3, 3, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 15, 15, 15] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 59 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/231 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCN(Cc2ccsc2)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1OC) `ZINC000488376286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488376286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000488376286 none COc1ccc(CCN(Cc2ccsc2)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 14, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 8, 8, 8, 4, 4, 3, 2, 3, 3, 6, 6, 6, 6, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 17, 16, 16, 16, 8, 8, 4, 4, 4, 4, 3, 3, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 17, 17, 17] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 64 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488376286 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286 Building ZINC000488376286 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488376286 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 230) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/230: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCN(Cc2ccsc2)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1OC) `ZINC000488376286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488376286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000488376286 none COc1ccc(CCN(Cc2ccsc2)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 14, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 8, 8, 8, 4, 4, 3, 2, 3, 3, 6, 6, 6, 6, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 15, 15, 15, 15, 8, 8, 4, 4, 4, 4, 3, 3, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 15, 15, 15] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 59 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 231) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCN(Cc2ccsc2)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1OC) `ZINC000488376286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488376286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000488376286 none COc1ccc(CCN(Cc2ccsc2)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 14, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 8, 8, 8, 4, 4, 3, 2, 3, 3, 6, 6, 6, 6, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 17, 16, 16, 16, 8, 8, 4, 4, 4, 4, 3, 3, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 17, 17, 17] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 64 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488376286 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488376286 Building ZINC000488418014 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488418014 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/232 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)cc1)C1CCOCC1) `ZINC000488418014.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488418014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000488418014 none CN(C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)cc1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 29, 5, 30, 3, 16, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 16, 16, 45, 50, 50, 50, 50, 50, 46, 46, 46, 16, 16, 3, 3, 3, 3, 3, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/233 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/233' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)cc1)C1CCOCC1) `ZINC000488418014.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488418014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000488418014 none CN(C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)cc1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 30, 4, 31, 5, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 2, 3, 3, 15, 15, 46, 50, 50, 50, 50, 50, 46, 46, 46, 15, 15, 3, 3, 3, 3, 3, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488418014 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014 Building ZINC000488418014 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488418014 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 232) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)cc1)C1CCOCC1) `ZINC000488418014.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488418014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000488418014 none CN(C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)cc1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 29, 5, 30, 3, 16, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 16, 16, 45, 50, 50, 50, 50, 50, 46, 46, 46, 16, 16, 3, 3, 3, 3, 3, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 233) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)cc1)C1CCOCC1) `ZINC000488418014.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488418014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000488418014 none CN(C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)cc1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 30, 4, 31, 5, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 2, 3, 3, 15, 15, 46, 50, 50, 50, 50, 50, 46, 46, 46, 15, 15, 3, 3, 3, 3, 3, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488418014 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488418014 Building ZINC000488441936 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488441936 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/234 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1) `ZINC000488441936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488441936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441936 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 22, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 41 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/235 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/235' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1) `ZINC000488441936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488441936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441936 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 3, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 24, 24, 3, 24, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 70 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/236 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/236' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1) `ZINC000488441936.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488441936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441936 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 22, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 41 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/237 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/237' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1) `ZINC000488441936.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488441936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441936 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 3, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 24, 24, 3, 24, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 70 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488441936 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 Building ZINC000488441936 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488441936 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 234) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/234: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1) `ZINC000488441936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488441936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441936 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 22, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 41 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 235) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/235: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1) `ZINC000488441936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488441936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441936 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 3, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 24, 24, 3, 24, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 70 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 236) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1) `ZINC000488441936.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488441936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441936 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 22, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 41 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 237) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1) `ZINC000488441936.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488441936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441936 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 3, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 24, 24, 3, 24, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 70 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488441936 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 Building ZINC000488441936 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488441936 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 234) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/234: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1) `ZINC000488441936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488441936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441936 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 22, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 41 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 235) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/235: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1) `ZINC000488441936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488441936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441936 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 3, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 24, 24, 3, 24, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 70 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 236) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1) `ZINC000488441936.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488441936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441936 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 22, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 41 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 237) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1) `ZINC000488441936.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488441936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441936 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 3, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 24, 24, 3, 24, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 70 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488441936 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 Building ZINC000488441936 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488441936 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 234) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/234: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1) `ZINC000488441936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488441936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441936 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 22, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 41 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 235) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/235: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1) `ZINC000488441936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488441936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441936 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 3, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 24, 24, 3, 24, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 70 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 236) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1) `ZINC000488441936.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488441936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441936 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 22, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 41 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 237) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1) `ZINC000488441936.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488441936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441936 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 3, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 24, 24, 3, 24, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 70 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488441936 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441936 Building ZINC000488441939 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488441939 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/238 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1) `ZINC000488441939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488441939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 2, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 62 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/239 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/239' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1) `ZINC000488441939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488441939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 43 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/240 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/240' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1) `ZINC000488441939.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488441939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 2, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 62 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/241 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/241' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1) `ZINC000488441939.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488441939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 43 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488441939 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 Building ZINC000488441939 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488441939 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 238) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1) `ZINC000488441939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488441939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 2, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 62 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 239) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1) `ZINC000488441939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488441939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 43 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 240) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1) `ZINC000488441939.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488441939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 2, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 62 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 241) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1) `ZINC000488441939.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488441939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 43 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488441939 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 Building ZINC000488441939 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488441939 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 238) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1) `ZINC000488441939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488441939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 2, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 62 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 239) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1) `ZINC000488441939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488441939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 43 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 240) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1) `ZINC000488441939.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488441939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 2, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 62 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 241) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1) `ZINC000488441939.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488441939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 43 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488441939 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 Building ZINC000488441939 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488441939 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 238) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1) `ZINC000488441939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488441939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 2, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 62 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 239) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1) `ZINC000488441939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488441939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 43 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 240) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1) `ZINC000488441939.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488441939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 2, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 62 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 241) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1) `ZINC000488441939.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488441939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 43 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488441939 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441939 Building ZINC000488441652 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488441652 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/242 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1) `ZINC000488441652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488441652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441652 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 9, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 11, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 66 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/243 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1) `ZINC000488441652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488441652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441652 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 2, 6, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 13, 13, 5, 13, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/244 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/244' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1) `ZINC000488441652.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488441652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441652 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 9, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 11, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 66 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/245 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/245' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1) `ZINC000488441652.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488441652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441652 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 2, 6, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 13, 13, 5, 13, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488441652 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 Building ZINC000488441652 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488441652 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 242) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1) `ZINC000488441652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488441652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441652 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 9, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 11, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 66 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 243) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1) `ZINC000488441652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488441652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441652 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 2, 6, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 13, 13, 5, 13, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 244) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1) `ZINC000488441652.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488441652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441652 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 9, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 11, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 66 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 245) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1) `ZINC000488441652.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488441652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441652 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 2, 6, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 13, 13, 5, 13, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488441652 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 Building ZINC000488441652 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488441652 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 242) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1) `ZINC000488441652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488441652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441652 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 9, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 11, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 66 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 243) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1) `ZINC000488441652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488441652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441652 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 2, 6, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 13, 13, 5, 13, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 244) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1) `ZINC000488441652.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488441652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441652 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 9, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 11, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 66 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 245) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1) `ZINC000488441652.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488441652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441652 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 2, 6, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 13, 13, 5, 13, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488441652 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 Building ZINC000488441652 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488441652 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 242) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1) `ZINC000488441652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488441652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441652 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 9, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 11, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 66 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 243) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1) `ZINC000488441652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488441652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441652 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 2, 6, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 13, 13, 5, 13, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 244) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1) `ZINC000488441652.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488441652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441652 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 9, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 11, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 66 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 245) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1) `ZINC000488441652.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488441652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441652 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 2, 6, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 13, 13, 5, 13, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488441652 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441652 Building ZINC000488441655 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488441655 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/246 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1) `ZINC000488441655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488441655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441655 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 22, 22, 22, 22, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 45 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/247 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/247' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1) `ZINC000488441655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488441655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441655 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 24, 24, 24, 24, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 42 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/248 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/248' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1) `ZINC000488441655.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488441655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441655 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 22, 22, 22, 22, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 45 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/249 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/249' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1) `ZINC000488441655.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488441655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441655 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 24, 24, 24, 24, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 42 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488441655 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 Building ZINC000488441655 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488441655 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 246) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1) `ZINC000488441655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488441655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441655 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 22, 22, 22, 22, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 45 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 247) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1) `ZINC000488441655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488441655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441655 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 24, 24, 24, 24, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 42 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 248) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1) `ZINC000488441655.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488441655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441655 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 22, 22, 22, 22, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 45 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 249) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1) `ZINC000488441655.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488441655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441655 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 24, 24, 24, 24, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 42 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488441655 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 Building ZINC000488441655 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488441655 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 246) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1) `ZINC000488441655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488441655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441655 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 22, 22, 22, 22, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 45 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 247) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1) `ZINC000488441655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488441655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441655 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 24, 24, 24, 24, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 42 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 248) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1) `ZINC000488441655.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488441655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441655 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 22, 22, 22, 22, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 45 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 249) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1) `ZINC000488441655.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488441655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441655 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 24, 24, 24, 24, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 42 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488441655 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 Building ZINC000488441655 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488441655 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 246) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1) `ZINC000488441655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488441655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441655 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 22, 22, 22, 22, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 45 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 247) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1) `ZINC000488441655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488441655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441655 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 24, 24, 24, 24, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 42 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 248) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1) `ZINC000488441655.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488441655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441655 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 22, 22, 22, 22, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 45 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 249) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1) `ZINC000488441655.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488441655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488441655 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 24, 24, 24, 24, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 42 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488441655 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488441655 Building ZINC000488481132 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488481132 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/250 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488481132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481132 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 24, 39, 39, 24, 39, 39, 12, 12, 12, 12, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 12, 12, 12, 12, 24, 24, 39, 39, 24, 39, 39, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/251 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488481132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481132 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 24, 45, 45, 24, 45, 45, 11, 11, 11, 11, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 11, 11, 11, 11, 24, 24, 45, 45, 24, 45, 45, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/252 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/252' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481132.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488481132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481132 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 24, 39, 39, 24, 39, 39, 12, 12, 12, 12, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 12, 12, 12, 12, 24, 24, 39, 39, 24, 39, 39, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/253 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/253' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481132.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488481132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481132 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 24, 45, 45, 24, 45, 45, 11, 11, 11, 11, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 11, 11, 11, 11, 24, 24, 45, 45, 24, 45, 45, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488481132 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 Building ZINC000488481132 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488481132 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 250) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/250: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488481132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481132 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 24, 39, 39, 24, 39, 39, 12, 12, 12, 12, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 12, 12, 12, 12, 24, 24, 39, 39, 24, 39, 39, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 251) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488481132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481132 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 24, 45, 45, 24, 45, 45, 11, 11, 11, 11, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 11, 11, 11, 11, 24, 24, 45, 45, 24, 45, 45, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 252) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481132.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488481132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481132 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 24, 39, 39, 24, 39, 39, 12, 12, 12, 12, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 12, 12, 12, 12, 24, 24, 39, 39, 24, 39, 39, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 253) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481132.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488481132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481132 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 24, 45, 45, 24, 45, 45, 11, 11, 11, 11, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 11, 11, 11, 11, 24, 24, 45, 45, 24, 45, 45, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488481132 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 Building ZINC000488481132 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488481132 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 250) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/250: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488481132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481132 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 24, 39, 39, 24, 39, 39, 12, 12, 12, 12, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 12, 12, 12, 12, 24, 24, 39, 39, 24, 39, 39, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 251) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488481132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481132 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 24, 45, 45, 24, 45, 45, 11, 11, 11, 11, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 11, 11, 11, 11, 24, 24, 45, 45, 24, 45, 45, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 252) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481132.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488481132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481132 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 24, 39, 39, 24, 39, 39, 12, 12, 12, 12, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 12, 12, 12, 12, 24, 24, 39, 39, 24, 39, 39, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 253) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481132.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488481132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481132 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 24, 45, 45, 24, 45, 45, 11, 11, 11, 11, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 11, 11, 11, 11, 24, 24, 45, 45, 24, 45, 45, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488481132 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 Building ZINC000488481132 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488481132 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 250) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/250: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488481132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481132 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 24, 39, 39, 24, 39, 39, 12, 12, 12, 12, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 12, 12, 12, 12, 24, 24, 39, 39, 24, 39, 39, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 251) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488481132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481132 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 24, 45, 45, 24, 45, 45, 11, 11, 11, 11, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 11, 11, 11, 11, 24, 24, 45, 45, 24, 45, 45, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 252) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481132.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488481132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481132 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 24, 39, 39, 24, 39, 39, 12, 12, 12, 12, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 12, 12, 12, 12, 24, 24, 39, 39, 24, 39, 39, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 253) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481132.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488481132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481132 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 24, 45, 45, 24, 45, 45, 11, 11, 11, 11, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 11, 11, 11, 11, 24, 24, 45, 45, 24, 45, 45, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488481132 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481132 Building ZINC000488481133 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488481133 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/254 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488481133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481133 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 25, 45, 45, 25, 45, 45, 12, 12, 12, 12, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 12, 12, 12, 12, 25, 25, 45, 45, 25, 45, 45, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/255 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488481133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481133 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 25, 44, 44, 25, 44, 44, 12, 12, 12, 12, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 12, 12, 12, 12, 25, 25, 44, 44, 25, 44, 44, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/256 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/256' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481133.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488481133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481133 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 25, 45, 45, 25, 45, 45, 12, 12, 12, 12, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 12, 12, 12, 12, 25, 25, 45, 45, 25, 45, 45, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/257 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/257' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481133.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488481133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481133 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 25, 44, 44, 25, 44, 44, 12, 12, 12, 12, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 12, 12, 12, 12, 25, 25, 44, 44, 25, 44, 44, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488481133 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 Building ZINC000488481133 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488481133 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 254) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/254: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488481133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481133 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 25, 45, 45, 25, 45, 45, 12, 12, 12, 12, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 12, 12, 12, 12, 25, 25, 45, 45, 25, 45, 45, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 255) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488481133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481133 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 25, 44, 44, 25, 44, 44, 12, 12, 12, 12, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 12, 12, 12, 12, 25, 25, 44, 44, 25, 44, 44, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 256) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481133.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488481133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481133 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 25, 45, 45, 25, 45, 45, 12, 12, 12, 12, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 12, 12, 12, 12, 25, 25, 45, 45, 25, 45, 45, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 257) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481133.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488481133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481133 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 25, 44, 44, 25, 44, 44, 12, 12, 12, 12, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 12, 12, 12, 12, 25, 25, 44, 44, 25, 44, 44, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488481133 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 Building ZINC000488481133 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488481133 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 254) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/254: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488481133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481133 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 25, 45, 45, 25, 45, 45, 12, 12, 12, 12, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 12, 12, 12, 12, 25, 25, 45, 45, 25, 45, 45, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 255) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488481133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481133 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 25, 44, 44, 25, 44, 44, 12, 12, 12, 12, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 12, 12, 12, 12, 25, 25, 44, 44, 25, 44, 44, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 256) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481133.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488481133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481133 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 25, 45, 45, 25, 45, 45, 12, 12, 12, 12, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 12, 12, 12, 12, 25, 25, 45, 45, 25, 45, 45, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 257) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481133.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488481133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481133 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 25, 44, 44, 25, 44, 44, 12, 12, 12, 12, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 12, 12, 12, 12, 25, 25, 44, 44, 25, 44, 44, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488481133 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 Building ZINC000488481133 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488481133 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 254) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/254: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488481133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481133 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 25, 45, 45, 25, 45, 45, 12, 12, 12, 12, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 12, 12, 12, 12, 25, 25, 45, 45, 25, 45, 45, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 255) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488481133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481133 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 25, 44, 44, 25, 44, 44, 12, 12, 12, 12, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 12, 12, 12, 12, 25, 25, 44, 44, 25, 44, 44, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 256) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481133.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488481133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481133 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 25, 45, 45, 25, 45, 45, 12, 12, 12, 12, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 12, 12, 12, 12, 25, 25, 45, 45, 25, 45, 45, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 257) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481133.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488481133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481133 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 25, 44, 44, 25, 44, 44, 12, 12, 12, 12, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 12, 12, 12, 12, 25, 25, 44, 44, 25, 44, 44, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488481133 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481133 Building ZINC000488481134 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488481134 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/258 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488481134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481134 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 13, 25, 43, 43, 33, 43, 43, 13, 13, 13, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 13, 13, 13, 13, 25, 25, 43, 43, 43, 43, 43, 13, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/259 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/259' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488481134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481134 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 21, 41, 41, 31, 41, 41, 11, 11, 11, 11, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 11, 11, 21, 21, 41, 41, 41, 41, 41, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/260 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/260' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481134.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488481134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481134 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 13, 25, 43, 43, 33, 43, 43, 13, 13, 13, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 13, 13, 13, 13, 25, 25, 43, 43, 43, 43, 43, 13, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/261 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/261' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481134.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488481134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481134 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 21, 41, 41, 31, 41, 41, 11, 11, 11, 11, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 11, 11, 21, 21, 41, 41, 41, 41, 41, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488481134 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 Building ZINC000488481134 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488481134 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 258) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488481134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481134 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 13, 25, 43, 43, 33, 43, 43, 13, 13, 13, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 13, 13, 13, 13, 25, 25, 43, 43, 43, 43, 43, 13, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 259) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488481134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481134 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 21, 41, 41, 31, 41, 41, 11, 11, 11, 11, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 11, 11, 21, 21, 41, 41, 41, 41, 41, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 260) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481134.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488481134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481134 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 13, 25, 43, 43, 33, 43, 43, 13, 13, 13, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 13, 13, 13, 13, 25, 25, 43, 43, 43, 43, 43, 13, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 261) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481134.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488481134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481134 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 21, 41, 41, 31, 41, 41, 11, 11, 11, 11, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 11, 11, 21, 21, 41, 41, 41, 41, 41, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488481134 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 Building ZINC000488481134 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488481134 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 258) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488481134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481134 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 13, 25, 43, 43, 33, 43, 43, 13, 13, 13, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 13, 13, 13, 13, 25, 25, 43, 43, 43, 43, 43, 13, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 259) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488481134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481134 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 21, 41, 41, 31, 41, 41, 11, 11, 11, 11, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 11, 11, 21, 21, 41, 41, 41, 41, 41, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 260) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481134.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488481134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481134 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 13, 25, 43, 43, 33, 43, 43, 13, 13, 13, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 13, 13, 13, 13, 25, 25, 43, 43, 43, 43, 43, 13, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 261) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481134.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488481134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481134 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 21, 41, 41, 31, 41, 41, 11, 11, 11, 11, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 11, 11, 21, 21, 41, 41, 41, 41, 41, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488481134 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 Building ZINC000488481134 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488481134 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 258) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488481134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481134 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 13, 25, 43, 43, 33, 43, 43, 13, 13, 13, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 13, 13, 13, 13, 25, 25, 43, 43, 43, 43, 43, 13, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 259) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488481134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481134 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 21, 41, 41, 31, 41, 41, 11, 11, 11, 11, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 11, 11, 21, 21, 41, 41, 41, 41, 41, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 260) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481134.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488481134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481134 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 13, 25, 43, 43, 33, 43, 43, 13, 13, 13, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 13, 13, 13, 13, 25, 25, 43, 43, 43, 43, 43, 13, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 261) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C) `ZINC000488481134.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488481134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481134 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2ccccc2)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 21, 41, 41, 31, 41, 41, 11, 11, 11, 11, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 11, 11, 21, 21, 41, 41, 41, 41, 41, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488481134 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481134 Building ZINC000488481135 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488481135 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/262 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481135.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488481135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481135 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 7, 11, 11, 11, 11, 11, 22, 41, 41, 22, 41, 41, 11, 11, 11, 11, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 11, 11, 22, 22, 41, 41, 22, 41, 41, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/263 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481135.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488481135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481135 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 7, 13, 13, 13, 13, 13, 25, 44, 44, 25, 44, 44, 13, 13, 13, 13, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 13, 13, 13, 13, 25, 25, 44, 44, 25, 44, 44, 13, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/264 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/264' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481135.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488481135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481135 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 7, 11, 11, 11, 11, 11, 22, 41, 41, 22, 41, 41, 11, 11, 11, 11, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 11, 11, 22, 22, 41, 41, 22, 41, 41, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/265 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/265' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481135.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488481135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481135 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 7, 13, 13, 13, 13, 13, 25, 44, 44, 25, 44, 44, 13, 13, 13, 13, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 13, 13, 13, 13, 25, 25, 44, 44, 25, 44, 44, 13, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488481135 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 Building ZINC000488481135 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488481135 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 262) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/262: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481135.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488481135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481135 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 7, 11, 11, 11, 11, 11, 22, 41, 41, 22, 41, 41, 11, 11, 11, 11, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 11, 11, 22, 22, 41, 41, 22, 41, 41, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 263) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481135.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488481135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481135 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 7, 13, 13, 13, 13, 13, 25, 44, 44, 25, 44, 44, 13, 13, 13, 13, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 13, 13, 13, 13, 25, 25, 44, 44, 25, 44, 44, 13, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 264) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481135.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488481135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481135 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 7, 11, 11, 11, 11, 11, 22, 41, 41, 22, 41, 41, 11, 11, 11, 11, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 11, 11, 22, 22, 41, 41, 22, 41, 41, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 265) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481135.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488481135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481135 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 7, 13, 13, 13, 13, 13, 25, 44, 44, 25, 44, 44, 13, 13, 13, 13, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 13, 13, 13, 13, 25, 25, 44, 44, 25, 44, 44, 13, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488481135 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 Building ZINC000488481135 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488481135 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 262) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/262: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481135.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488481135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481135 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 7, 11, 11, 11, 11, 11, 22, 41, 41, 22, 41, 41, 11, 11, 11, 11, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 11, 11, 22, 22, 41, 41, 22, 41, 41, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 263) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481135.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488481135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481135 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 7, 13, 13, 13, 13, 13, 25, 44, 44, 25, 44, 44, 13, 13, 13, 13, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 13, 13, 13, 13, 25, 25, 44, 44, 25, 44, 44, 13, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 264) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481135.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488481135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481135 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 7, 11, 11, 11, 11, 11, 22, 41, 41, 22, 41, 41, 11, 11, 11, 11, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 11, 11, 22, 22, 41, 41, 22, 41, 41, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 265) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481135.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488481135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481135 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 7, 13, 13, 13, 13, 13, 25, 44, 44, 25, 44, 44, 13, 13, 13, 13, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 13, 13, 13, 13, 25, 25, 44, 44, 25, 44, 44, 13, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488481135 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 Building ZINC000488481135 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488481135 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 262) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/262: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481135.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488481135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481135 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 7, 11, 11, 11, 11, 11, 22, 41, 41, 22, 41, 41, 11, 11, 11, 11, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 11, 11, 22, 22, 41, 41, 22, 41, 41, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 263) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481135.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488481135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481135 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 7, 13, 13, 13, 13, 13, 25, 44, 44, 25, 44, 44, 13, 13, 13, 13, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 13, 13, 13, 13, 25, 25, 44, 44, 25, 44, 44, 13, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 264) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481135.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488481135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481135 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 7, 11, 11, 11, 11, 11, 22, 41, 41, 22, 41, 41, 11, 11, 11, 11, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 11, 11, 22, 22, 41, 41, 22, 41, 41, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 265) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C) `ZINC000488481135.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488481135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000488481135 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2ccccc2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 7, 13, 13, 13, 13, 13, 25, 44, 44, 25, 44, 44, 13, 13, 13, 13, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 13, 13, 13, 13, 25, 25, 44, 44, 25, 44, 44, 13, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488481135 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488481135 Building ZINC000488663751 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488663751 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/266 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCc2c[nH]nc21) `ZINC000488663751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488663751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488663751 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCc2c[nH]nc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 6, 6, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 18, 18, 3, 18, 3, 3, 3, 6, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 69 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/267 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCc2c[nH]nc21) `ZINC000488663751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488663751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488663751 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCc2c[nH]nc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 34, 34, 10, 34, 34, 34, 34, 34, 34, 4, 4, 1, 1, 1, 1, 3, 3, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 34, 34, 10, 34, 4, 4, 4, 3, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 91 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488663751 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751 Building ZINC000488663751 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488663751 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 266) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/266: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCc2c[nH]nc21) `ZINC000488663751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488663751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488663751 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCc2c[nH]nc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 6, 6, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 18, 18, 3, 18, 3, 3, 3, 6, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 69 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 267) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/267: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCc2c[nH]nc21) `ZINC000488663751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488663751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488663751 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCc2c[nH]nc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 34, 34, 10, 34, 34, 34, 34, 34, 34, 4, 4, 1, 1, 1, 1, 3, 3, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 34, 34, 10, 34, 4, 4, 4, 3, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 91 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488663751 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663751 Building ZINC000488663752 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488663752 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/268 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2c[nH]nc21) `ZINC000488663752.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488663752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488663752 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2c[nH]nc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 34, 34, 4, 34, 34, 34, 34, 34, 34, 4, 4, 1, 1, 1, 1, 3, 3, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 34, 34, 4, 34, 4, 4, 4, 3, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 93 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/269 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2c[nH]nc21) `ZINC000488663752.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488663752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488663752 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2c[nH]nc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 17, 17, 2, 17, 17, 17, 17, 17, 17, 2, 2, 1, 1, 1, 1, 6, 6, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 17, 17, 2, 17, 2, 2, 2, 6, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 65 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488663752 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752 Building ZINC000488663752 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488663752 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 268) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/268: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2c[nH]nc21) `ZINC000488663752.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488663752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488663752 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2c[nH]nc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 34, 34, 4, 34, 34, 34, 34, 34, 34, 4, 4, 1, 1, 1, 1, 3, 3, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 34, 34, 4, 34, 4, 4, 4, 3, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 93 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 269) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/269: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2c[nH]nc21) `ZINC000488663752.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488663752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488663752 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2c[nH]nc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 17, 17, 2, 17, 17, 17, 17, 17, 17, 2, 2, 1, 1, 1, 1, 6, 6, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 17, 17, 2, 17, 2, 2, 2, 6, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 65 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488663752 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488663752 Building ZINC000488934388 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488934388 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/270 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(F)cc2)CC1) `ZINC000488934388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488934388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488934388 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 26, 41, 41, 26, 41, 41, 41, 13, 13, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 13, 13, 13, 13, 26, 26, 41, 41, 41, 41, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/271 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(F)cc2)CC1) `ZINC000488934388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488934388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488934388 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 27, 44, 44, 38, 44, 44, 44, 13, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 13, 13, 13, 13, 27, 27, 44, 44, 44, 44, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/272 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/272' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(F)cc2)CC1) `ZINC000488934388.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488934388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488934388 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 25, 43, 43, 34, 35, 43, 43, 12, 12, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 12, 12, 12, 12, 25, 25, 43, 43, 43, 43, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/273 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/273' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(F)cc2)CC1) `ZINC000488934388.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488934388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488934388 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 26, 43, 43, 35, 42, 43, 43, 12, 12, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 12, 12, 12, 12, 26, 26, 43, 43, 43, 43, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488934388 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 Building ZINC000488934388 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488934388 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 270) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/270: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(F)cc2)CC1) `ZINC000488934388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488934388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488934388 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 26, 41, 41, 26, 41, 41, 41, 13, 13, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 13, 13, 13, 13, 26, 26, 41, 41, 41, 41, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 271) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(F)cc2)CC1) `ZINC000488934388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488934388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488934388 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 27, 44, 44, 38, 44, 44, 44, 13, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 13, 13, 13, 13, 27, 27, 44, 44, 44, 44, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 272) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/272: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(F)cc2)CC1) `ZINC000488934388.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488934388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488934388 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 25, 43, 43, 34, 35, 43, 43, 12, 12, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 12, 12, 12, 12, 25, 25, 43, 43, 43, 43, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 273) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/273: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(F)cc2)CC1) `ZINC000488934388.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488934388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488934388 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 26, 43, 43, 35, 42, 43, 43, 12, 12, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 12, 12, 12, 12, 26, 26, 43, 43, 43, 43, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488934388 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 Building ZINC000488934388 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488934388 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 270) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/270: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(F)cc2)CC1) `ZINC000488934388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488934388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488934388 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 26, 41, 41, 26, 41, 41, 41, 13, 13, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 13, 13, 13, 13, 26, 26, 41, 41, 41, 41, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 271) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(F)cc2)CC1) `ZINC000488934388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488934388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488934388 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 27, 44, 44, 38, 44, 44, 44, 13, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 13, 13, 13, 13, 27, 27, 44, 44, 44, 44, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 272) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/272: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(F)cc2)CC1) `ZINC000488934388.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488934388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488934388 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 25, 43, 43, 34, 35, 43, 43, 12, 12, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 12, 12, 12, 12, 25, 25, 43, 43, 43, 43, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 273) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/273: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(F)cc2)CC1) `ZINC000488934388.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488934388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488934388 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 26, 43, 43, 35, 42, 43, 43, 12, 12, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 12, 12, 12, 12, 26, 26, 43, 43, 43, 43, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488934388 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 Building ZINC000488934388 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000488934388 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 270) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/270: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(F)cc2)CC1) `ZINC000488934388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488934388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488934388 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 26, 41, 41, 26, 41, 41, 41, 13, 13, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 13, 13, 13, 13, 26, 26, 41, 41, 41, 41, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 271) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(F)cc2)CC1) `ZINC000488934388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488934388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488934388 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 27, 44, 44, 38, 44, 44, 44, 13, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 13, 13, 13, 13, 27, 27, 44, 44, 44, 44, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 272) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/272: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(F)cc2)CC1) `ZINC000488934388.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000488934388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488934388 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 25, 43, 43, 34, 35, 43, 43, 12, 12, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 12, 12, 12, 12, 25, 25, 43, 43, 43, 43, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 273) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/273: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(F)cc2)CC1) `ZINC000488934388.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000488934388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000488934388 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 26, 43, 43, 35, 42, 43, 43, 12, 12, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 12, 12, 12, 12, 26, 26, 43, 43, 43, 43, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000488934388 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000488934388 Building ZINC000489032864 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489032864 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/274 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)N(CC(=O)Nc1cccc(C)c1C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000489032864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489032864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000489032864 none CC[C@@H](C)N(CC(=O)Nc1cccc(C)c1C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 2, 2, 2, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 4, 4, 4, 2, 2, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 62 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/275 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)N(CC(=O)Nc1cccc(C)c1C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000489032864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489032864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000489032864 none CC[C@@H](C)N(CC(=O)Nc1cccc(C)c1C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 2, 5, 5, 2, 2, 2, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 5, 5, 5, 2, 2, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 69 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489032864 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864 Building ZINC000489032864 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489032864 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 274) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/274: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)N(CC(=O)Nc1cccc(C)c1C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000489032864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489032864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000489032864 none CC[C@@H](C)N(CC(=O)Nc1cccc(C)c1C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 2, 2, 2, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 4, 4, 4, 2, 2, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 62 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 275) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/275: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)N(CC(=O)Nc1cccc(C)c1C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000489032864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489032864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000489032864 none CC[C@@H](C)N(CC(=O)Nc1cccc(C)c1C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 2, 5, 5, 2, 2, 2, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 5, 5, 5, 2, 2, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 69 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489032864 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032864 Building ZINC000489032869 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489032869 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/276 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)N(CC(=O)Nc1cccc(C)c1C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000489032869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489032869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000489032869 none CC[C@H](C)N(CC(=O)Nc1cccc(C)c1C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 2, 5, 5, 2, 2, 2, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 5, 5, 5, 2, 2, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 69 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/277 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)N(CC(=O)Nc1cccc(C)c1C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000489032869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489032869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000489032869 none CC[C@H](C)N(CC(=O)Nc1cccc(C)c1C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 2, 2, 2, 5, 5, 5, 14, 14, 5, 14, 14, 14, 14, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 4, 4, 4, 2, 2, 5, 14, 14, 5, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 78 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489032869 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869 Building ZINC000489032869 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489032869 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 276) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)N(CC(=O)Nc1cccc(C)c1C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000489032869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489032869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000489032869 none CC[C@H](C)N(CC(=O)Nc1cccc(C)c1C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 2, 5, 5, 2, 2, 2, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 5, 5, 5, 2, 2, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 69 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 277) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)N(CC(=O)Nc1cccc(C)c1C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000489032869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489032869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000489032869 none CC[C@H](C)N(CC(=O)Nc1cccc(C)c1C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 2, 2, 2, 5, 5, 5, 14, 14, 5, 14, 14, 14, 14, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 4, 4, 4, 2, 2, 5, 14, 14, 5, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 78 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489032869 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489032869 Building ZINC000489058863 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489058863 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/278 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H](N(C)C)C1) `ZINC000489058863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489058863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000489058863 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 12, 12, 8, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 71 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/279 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H](N(C)C)C1) `ZINC000489058863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489058863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000489058863 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 19, 19, 3, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 16, 16, 9, 3, 3, 3, 19, 19, 5, 19, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 97 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489058863 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863 Building ZINC000489058863 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489058863 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 278) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/278: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H](N(C)C)C1) `ZINC000489058863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489058863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000489058863 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 12, 12, 8, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 71 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 279) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/279: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H](N(C)C)C1) `ZINC000489058863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489058863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000489058863 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 19, 19, 3, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 16, 16, 9, 3, 3, 3, 19, 19, 5, 19, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 97 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489058863 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058863 Building ZINC000489058864 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489058864 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/280 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H](N(C)C)C1) `ZINC000489058864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489058864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000489058864 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 17, 17, 9, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 3, 3, 4, 10, 10, 10, 10, 10, 10, 10, 13, 13, 10, 3, 3, 3, 17, 17, 12, 17, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 85 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/281 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/281' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H](N(C)C)C1) `ZINC000489058864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489058864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000489058864 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 17, 17, 4, 17, 17, 17, 17, 17, 17, 4, 4, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 9, 9, 11, 11, 9, 4, 4, 4, 17, 17, 4, 17, 4, 4, 4, 2, 9, 9, 9, 9, 9, 9, 11, 11, 11, 11, 11, 11, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 70 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489058864 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864 Building ZINC000489058864 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489058864 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 280) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H](N(C)C)C1) `ZINC000489058864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489058864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000489058864 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 17, 17, 9, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 3, 3, 4, 10, 10, 10, 10, 10, 10, 10, 13, 13, 10, 3, 3, 3, 17, 17, 12, 17, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 85 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 281) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H](N(C)C)C1) `ZINC000489058864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489058864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000489058864 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 17, 17, 4, 17, 17, 17, 17, 17, 17, 4, 4, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 9, 9, 11, 11, 9, 4, 4, 4, 17, 17, 4, 17, 4, 4, 4, 2, 9, 9, 9, 9, 9, 9, 11, 11, 11, 11, 11, 11, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 70 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489058864 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058864 Building ZINC000489058865 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489058865 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/282 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H](N(C)C)C1) `ZINC000489058865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489058865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000489058865 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 11, 11, 9, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 4, 9, 9, 9, 9, 9, 9, 11, 11, 11, 11, 11, 11, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 67 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/283 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/283' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H](N(C)C)C1) `ZINC000489058865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489058865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000489058865 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 17, 17, 4, 17, 17, 17, 17, 17, 17, 4, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 12, 12, 9, 4, 4, 4, 17, 17, 6, 17, 4, 4, 4, 3, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 81 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489058865 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865 Building ZINC000489058865 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489058865 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 282) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/282: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H](N(C)C)C1) `ZINC000489058865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489058865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000489058865 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 11, 11, 9, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 4, 9, 9, 9, 9, 9, 9, 11, 11, 11, 11, 11, 11, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 67 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 283) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/283: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H](N(C)C)C1) `ZINC000489058865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489058865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000489058865 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 17, 17, 4, 17, 17, 17, 17, 17, 17, 4, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 12, 12, 9, 4, 4, 4, 17, 17, 6, 17, 4, 4, 4, 3, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 81 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489058865 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058865 Building ZINC000489058866 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489058866 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/284 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H](N(C)C)C1) `ZINC000489058866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489058866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000489058866 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 13, 13, 10, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 4, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 73 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/285 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H](N(C)C)C1) `ZINC000489058866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489058866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000489058866 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 5, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 11, 11, 8, 3, 3, 3, 15, 15, 12, 15, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11, 11, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 83 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489058866 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866 Building ZINC000489058866 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489058866 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 284) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H](N(C)C)C1) `ZINC000489058866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489058866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000489058866 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 13, 13, 10, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 4, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 73 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 285) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H](N(C)C)C1) `ZINC000489058866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489058866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000489058866 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 5, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 11, 11, 8, 3, 3, 3, 15, 15, 12, 15, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11, 11, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 83 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489058866 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489058866 Building ZINC000489132770 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489132770 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/286 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCOC2(CCC2)C1) `ZINC000489132770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489132770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000489132770 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCOC2(CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 6, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 14, 14, 7, 14, 3, 3, 3, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 70 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/287 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCOC2(CCC2)C1) `ZINC000489132770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489132770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000489132770 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCOC2(CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489132770 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770 Building ZINC000489132770 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489132770 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 286) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/286: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCOC2(CCC2)C1) `ZINC000489132770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489132770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000489132770 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCOC2(CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 6, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 14, 14, 7, 14, 3, 3, 3, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 70 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 287) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/287: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCOC2(CCC2)C1) `ZINC000489132770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489132770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000489132770 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCOC2(CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489132770 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132770 Building ZINC000489132772 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489132772 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/288 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOC2(CCC2)C1) `ZINC000489132772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489132772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000489132772 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOC2(CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 42 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/289 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOC2(CCC2)C1) `ZINC000489132772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489132772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000489132772 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOC2(CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 61 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489132772 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772 Building ZINC000489132772 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489132772 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 288) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/288: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOC2(CCC2)C1) `ZINC000489132772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489132772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000489132772 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOC2(CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 42 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 289) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/289: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOC2(CCC2)C1) `ZINC000489132772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489132772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000489132772 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOC2(CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 61 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489132772 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489132772 Building ZINC000489405002 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489405002 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/290 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnn(c2ncc(Cl)cc2Cl)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000489405002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489405002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000489405002 none O=C(Nc1cnn(c2ncc(Cl)cc2Cl)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 8, 1, 8, 1, 1, 16, 1, 1, 16, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 13, 26, 26, 26, 26, 26, 26, 26, 13, 1, 1, 1, 9, 9, 9, 9, 12, 12, 9, 12, 12, 9, 3, 13, 26, 26, 13, 9, 12, 12, 9, 12, 12, 9] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/291 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnn(c2ncc(Cl)cc2Cl)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000489405002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489405002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000489405002 none O=C(Nc1cnn(c2ncc(Cl)cc2Cl)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 8, 1, 8, 1, 1, 16, 1, 1, 16, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 13, 26, 26, 26, 26, 26, 26, 26, 13, 1, 1, 1, 10, 10, 10, 10, 13, 13, 10, 13, 13, 10, 3, 13, 26, 26, 13, 10, 13, 13, 10, 13, 13, 10] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489405002 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002 Building ZINC000489405002 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489405002 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 290) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/290: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnn(c2ncc(Cl)cc2Cl)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000489405002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489405002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000489405002 none O=C(Nc1cnn(c2ncc(Cl)cc2Cl)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 8, 1, 8, 1, 1, 16, 1, 1, 16, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 13, 26, 26, 26, 26, 26, 26, 26, 13, 1, 1, 1, 9, 9, 9, 9, 12, 12, 9, 12, 12, 9, 3, 13, 26, 26, 13, 9, 12, 12, 9, 12, 12, 9] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 291) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/291: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnn(c2ncc(Cl)cc2Cl)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000489405002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489405002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000489405002 none O=C(Nc1cnn(c2ncc(Cl)cc2Cl)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 8, 1, 8, 1, 1, 16, 1, 1, 16, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 13, 26, 26, 26, 26, 26, 26, 26, 13, 1, 1, 1, 10, 10, 10, 10, 13, 13, 10, 13, 13, 10, 3, 13, 26, 26, 13, 10, 13, 13, 10, 13, 13, 10] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489405002 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489405002 Building ZINC000489467625 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489467625 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/292 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2c(ncn2c2ccc(C)cc2)C1) `ZINC000489467625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489467625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000489467625 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2c(ncn2c2ccc(C)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 7, 10, 10, 4, 4, 1, 1, 1, 1, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 13, 4, 4, 4, 10, 10, 7, 10, 10, 4, 4, 4, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 20, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 58 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/293 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2c(ncn2c2ccc(C)cc2)C1) `ZINC000489467625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489467625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000489467625 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2c(ncn2c2ccc(C)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 1, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 13, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 20, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 63 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489467625 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625 Building ZINC000489467625 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489467625 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 292) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/292: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2c(ncn2c2ccc(C)cc2)C1) `ZINC000489467625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489467625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000489467625 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2c(ncn2c2ccc(C)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 7, 10, 10, 4, 4, 1, 1, 1, 1, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 13, 4, 4, 4, 10, 10, 7, 10, 10, 4, 4, 4, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 20, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 58 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 293) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/293: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2c(ncn2c2ccc(C)cc2)C1) `ZINC000489467625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489467625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000489467625 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2c(ncn2c2ccc(C)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 1, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 13, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 20, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 63 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489467625 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489467625 Building ZINC000489538425 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489538425 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/294 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCSC[C@H](C)C1) `ZINC000489538425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489538425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000489538425 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCSC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 25, 25, 3, 25, 25, 25, 25, 25, 25, 3, 3, 1, 1, 1, 1, 6, 7, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 25, 25, 3, 25, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 74 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/295 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/295' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCSC[C@H](C)C1) `ZINC000489538425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489538425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000489538425 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCSC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 10, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 2, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 18, 18, 18, 18, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 62 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489538425 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425 Building ZINC000489538425 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489538425 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 294) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/294: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCSC[C@H](C)C1) `ZINC000489538425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489538425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000489538425 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCSC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 25, 25, 3, 25, 25, 25, 25, 25, 25, 3, 3, 1, 1, 1, 1, 6, 7, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 25, 25, 3, 25, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 74 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 295) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/295: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCSC[C@H](C)C1) `ZINC000489538425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489538425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000489538425 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCSC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 10, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 2, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 18, 18, 18, 18, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 62 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489538425 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538425 Building ZINC000489538426 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489538426 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/296 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCSC[C@@H](C)C1) `ZINC000489538426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489538426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000489538426 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCSC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 24, 24, 24, 24, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 44 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/297 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/297' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCSC[C@@H](C)C1) `ZINC000489538426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489538426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000489538426 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCSC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 25, 25, 3, 25, 25, 25, 25, 25, 25, 3, 3, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 25, 25, 3, 25, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 75 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489538426 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426 Building ZINC000489538426 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489538426 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 296) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCSC[C@@H](C)C1) `ZINC000489538426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489538426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000489538426 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCSC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 24, 24, 24, 24, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 44 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 297) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCSC[C@@H](C)C1) `ZINC000489538426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489538426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000489538426 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCSC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 25, 25, 3, 25, 25, 25, 25, 25, 25, 3, 3, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 25, 25, 3, 25, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 75 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489538426 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489538426 Building ZINC000489593039 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489593039 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/298 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(S(=O)(=O)NCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000489593039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489593039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000489593039 none O=C(Nc1ccc(S(=O)(=O)NCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 5, 2, 5, 9, 9, 9, 16, 50, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 5, 5, 16, 50, 50, 50, 50, 50, 50, 50, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/299 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(S(=O)(=O)NCc2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000489593039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489593039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000489593039 none O=C(Nc1ccc(S(=O)(=O)NCc2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 4, 8, 8, 8, 15, 50, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 4, 4, 15, 50, 50, 50, 50, 50, 50, 50, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489593039 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039 Building ZINC000489593039 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489593039 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 298) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/298: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(S(=O)(=O)NCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000489593039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489593039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000489593039 none O=C(Nc1ccc(S(=O)(=O)NCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 5, 2, 5, 9, 9, 9, 16, 50, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 5, 5, 16, 50, 50, 50, 50, 50, 50, 50, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 299) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(S(=O)(=O)NCc2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000489593039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489593039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000489593039 none O=C(Nc1ccc(S(=O)(=O)NCc2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 4, 8, 8, 8, 15, 50, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 4, 4, 15, 50, 50, 50, 50, 50, 50, 50, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489593039 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489593039 Building ZINC000489692330 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489692330 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/300 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)Cc1ccncc1) `ZINC000489692330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489692330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489692330 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)Cc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 13, 13, 13, 13, 13, 13, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 2, 7, 7, 7, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/301 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/301' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)Cc1ccncc1) `ZINC000489692330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489692330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489692330 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)Cc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 6, 6, 6, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 77 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489692330 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330 Building ZINC000489692330 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489692330 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 300) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)Cc1ccncc1) `ZINC000489692330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489692330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489692330 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)Cc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 13, 13, 13, 13, 13, 13, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 2, 7, 7, 7, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 301) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)Cc1ccncc1) `ZINC000489692330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489692330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489692330 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)Cc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 6, 6, 6, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 77 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489692330 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692330 Building ZINC000489692331 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489692331 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/302 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1ccncc1) `ZINC000489692331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489692331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489692331 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 6, 6, 6, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 83 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/303 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1ccncc1) `ZINC000489692331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489692331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489692331 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 14, 14, 14, 14, 14, 14, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 2, 7, 7, 7, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489692331 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331 Building ZINC000489692331 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489692331 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 302) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/302: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1ccncc1) `ZINC000489692331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489692331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489692331 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 6, 6, 6, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 83 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 303) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/303: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1ccncc1) `ZINC000489692331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489692331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489692331 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 14, 14, 14, 14, 14, 14, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 2, 7, 7, 7, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000489692331 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000489692331 Building ZINC000490276303 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490276303 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/304 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(c2noc(C(F)(F)F)n2)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000490276303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490276303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000490276303 none O=C(Nc1cccc(c2noc(C(F)(F)F)n2)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 15, 15, 15, 8, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 9, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/305 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(c2noc(C(F)(F)F)n2)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000490276303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490276303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000490276303 none O=C(Nc1cccc(c2noc(C(F)(F)F)n2)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 15, 15, 15, 8, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 9, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000490276303 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303 Building ZINC000490276303 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490276303 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 304) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/304: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(c2noc(C(F)(F)F)n2)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000490276303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490276303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000490276303 none O=C(Nc1cccc(c2noc(C(F)(F)F)n2)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 15, 15, 15, 8, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 9, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 305) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/305: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(c2noc(C(F)(F)F)n2)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000490276303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490276303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000490276303 none O=C(Nc1cccc(c2noc(C(F)(F)F)n2)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 15, 15, 15, 8, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 9, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000490276303 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490276303 Building ZINC000490790329 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490790329 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/306 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3ccc(F)cc3F)cc2)cc1) `ZINC000490790329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490790329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000490790329 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3ccc(F)cc3F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 3, 4, 12, 12, 12, 30, 50, 50, 46, 50, 50, 50, 50, 7, 7, 2, 2, 2, 2, 2, 2, 2, 3, 7, 7, 30, 50, 50, 50, 7, 7, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/307 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3ccc(F)cc3F)cc2)cc1) `ZINC000490790329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490790329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000490790329 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3ccc(F)cc3F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 10, 10, 10, 29, 50, 50, 50, 50, 50, 50, 50, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 29, 50, 50, 50, 5, 5, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000490790329 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329 Building ZINC000490790329 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490790329 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 306) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/306: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3ccc(F)cc3F)cc2)cc1) `ZINC000490790329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490790329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000490790329 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3ccc(F)cc3F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 3, 4, 12, 12, 12, 30, 50, 50, 46, 50, 50, 50, 50, 7, 7, 2, 2, 2, 2, 2, 2, 2, 3, 7, 7, 30, 50, 50, 50, 7, 7, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 307) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3ccc(F)cc3F)cc2)cc1) `ZINC000490790329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490790329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000490790329 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3ccc(F)cc3F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 10, 10, 10, 29, 50, 50, 50, 50, 50, 50, 50, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 29, 50, 50, 50, 5, 5, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000490790329 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490790329 Building ZINC000490976119 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490976119 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/308 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)c(OC)cc2OC)cc1Cl) `ZINC000490976119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490976119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000490976119 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)c(OC)cc2OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 12, 5, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 6, 13, 6, 6, 6, 10, 6, 6, 6, 12, 12, 12, 6, 6, 2, 6, 13, 13, 13, 6, 10, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/309 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)c(OC)cc2OC)cc1Cl) `ZINC000490976119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490976119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000490976119 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)c(OC)cc2OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 12, 5, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 6, 13, 6, 6, 6, 10, 6, 6, 6, 12, 12, 12, 6, 6, 2, 6, 13, 13, 13, 6, 10, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000490976119 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119 Building ZINC000490976119 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490976119 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 308) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/308: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)c(OC)cc2OC)cc1Cl) `ZINC000490976119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490976119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000490976119 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)c(OC)cc2OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 12, 5, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 6, 13, 6, 6, 6, 10, 6, 6, 6, 12, 12, 12, 6, 6, 2, 6, 13, 13, 13, 6, 10, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 309) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)c(OC)cc2OC)cc1Cl) `ZINC000490976119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490976119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000490976119 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)c(OC)cc2OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 12, 5, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 6, 13, 6, 6, 6, 10, 6, 6, 6, 12, 12, 12, 6, 6, 2, 6, 13, 13, 13, 6, 10, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000490976119 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000490976119 Building ZINC000491029765 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000491029765 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/310 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1nc2ccc(I)cc2s1) `ZINC000491029765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000491029765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000491029765 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1nc2ccc(I)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 18, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 2, 8, 8, 1, 1, 1, 1, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 8, 8, 8, 8, 11, 20, 20, 20] 38 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/311 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1nc2ccc(I)cc2s1) `ZINC000491029765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000491029765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000491029765 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1nc2ccc(I)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 18, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 2, 8, 8, 1, 1, 1, 1, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 8, 8, 8, 8, 11, 20, 20, 20] 38 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000491029765 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765 Building ZINC000491029765 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000491029765 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 310) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1nc2ccc(I)cc2s1) `ZINC000491029765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000491029765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000491029765 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1nc2ccc(I)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 18, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 2, 8, 8, 1, 1, 1, 1, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 8, 8, 8, 8, 11, 20, 20, 20] 38 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 311) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1nc2ccc(I)cc2s1) `ZINC000491029765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000491029765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000491029765 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1nc2ccc(I)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 18, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 2, 8, 8, 1, 1, 1, 1, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 8, 8, 8, 8, 11, 20, 20, 20] 38 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000491029765 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491029765 Building ZINC000491112844 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000491112844 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/312 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1S(=O)(=O)C1CCCC1) `ZINC000491112844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000491112844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000491112844 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1S(=O)(=O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 22, 22, 31, 35, 35, 35, 35, 12, 12, 12, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 12, 35, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 149 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/313 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1S(=O)(=O)C1CCCC1) `ZINC000491112844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000491112844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000491112844 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1S(=O)(=O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 21, 21, 30, 35, 35, 35, 35, 12, 12, 12, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 12, 35, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 150 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000491112844 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844 Building ZINC000491112844 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000491112844 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 312) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1S(=O)(=O)C1CCCC1) `ZINC000491112844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000491112844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000491112844 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1S(=O)(=O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 22, 22, 31, 35, 35, 35, 35, 12, 12, 12, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 12, 35, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 149 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 313) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1S(=O)(=O)C1CCCC1) `ZINC000491112844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000491112844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000491112844 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1S(=O)(=O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 21, 21, 30, 35, 35, 35, 35, 12, 12, 12, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 12, 35, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 150 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000491112844 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491112844 Building ZINC000760637260 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760637260 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/314 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cnc3c(c2)CN(C(=O)OC(C)(C)C)CC3)cc1Cl) `ZINC000760637260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760637260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000760637260 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cnc3c(c2)CN(C(=O)OC(C)(C)C)CC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 16, 16, 8, 8, 16, 16, 16, 22, 22, 22, 22, 22, 22, 16, 16, 4, 4, 4, 8, 8, 8, 4, 4, 2, 16, 8, 16, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 16, 16, 16, 16, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/315 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/315' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cnc3c(c2)CN(C(=O)OC(C)(C)C)CC3)cc1Cl) `ZINC000760637260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760637260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000760637260 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cnc3c(c2)CN(C(=O)OC(C)(C)C)CC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 16, 16, 8, 8, 16, 16, 16, 22, 22, 22, 22, 22, 22, 16, 16, 4, 4, 4, 8, 8, 8, 4, 4, 2, 16, 8, 16, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 16, 16, 16, 16, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760637260 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260 Building ZINC000760637260 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760637260 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 314) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cnc3c(c2)CN(C(=O)OC(C)(C)C)CC3)cc1Cl) `ZINC000760637260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760637260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000760637260 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cnc3c(c2)CN(C(=O)OC(C)(C)C)CC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 16, 16, 8, 8, 16, 16, 16, 22, 22, 22, 22, 22, 22, 16, 16, 4, 4, 4, 8, 8, 8, 4, 4, 2, 16, 8, 16, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 16, 16, 16, 16, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 315) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/315: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cnc3c(c2)CN(C(=O)OC(C)(C)C)CC3)cc1Cl) `ZINC000760637260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760637260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000760637260 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cnc3c(c2)CN(C(=O)OC(C)(C)C)CC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 16, 16, 8, 8, 16, 16, 16, 22, 22, 22, 22, 22, 22, 16, 16, 4, 4, 4, 8, 8, 8, 4, 4, 2, 16, 8, 16, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 16, 16, 16, 16, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760637260 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760637260 Building ZINC000760648274 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760648274 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/316 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](NC(=O)OC(C)(C)C)[C@@H]3C2)cc1Cl) `ZINC000760648274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760648274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760648274 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](NC(=O)OC(C)(C)C)[C@@H]3C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 21, 21, 29, 29, 29, 29, 6, 6, 6, 2, 2, 2, 5, 5, 5, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 2] 50 rigid atoms, others: [8, 9, 5, 6, 7] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/317 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](NC(=O)OC(C)(C)C)[C@@H]3C2)cc1Cl) `ZINC000760648274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760648274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760648274 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](NC(=O)OC(C)(C)C)[C@@H]3C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 2, 3, 3, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 21, 21, 30, 30, 30, 30, 5, 5, 5, 3, 3, 3, 7, 7, 7, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760648274 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274 Building ZINC000760648274 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760648274 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 316) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/316: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](NC(=O)OC(C)(C)C)[C@@H]3C2)cc1Cl) `ZINC000760648274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760648274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760648274 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](NC(=O)OC(C)(C)C)[C@@H]3C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 21, 21, 29, 29, 29, 29, 6, 6, 6, 2, 2, 2, 5, 5, 5, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 2] 50 rigid atoms, others: [8, 9, 5, 6, 7] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 317) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/317: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](NC(=O)OC(C)(C)C)[C@@H]3C2)cc1Cl) `ZINC000760648274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760648274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760648274 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](NC(=O)OC(C)(C)C)[C@@H]3C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 2, 3, 3, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 21, 21, 30, 30, 30, 30, 5, 5, 5, 3, 3, 3, 7, 7, 7, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760648274 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648274 Building ZINC000760648275 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760648275 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/318 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](NC(=O)OC(C)(C)C)[C@H]3C2)cc1Cl) `ZINC000760648275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760648275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760648275 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](NC(=O)OC(C)(C)C)[C@H]3C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 19, 19, 26, 26, 26, 26, 4, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/319 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/319' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](NC(=O)OC(C)(C)C)[C@H]3C2)cc1Cl) `ZINC000760648275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760648275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760648275 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](NC(=O)OC(C)(C)C)[C@H]3C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 17, 17, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760648275 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275 Building ZINC000760648275 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760648275 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 318) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/318: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](NC(=O)OC(C)(C)C)[C@H]3C2)cc1Cl) `ZINC000760648275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760648275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760648275 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](NC(=O)OC(C)(C)C)[C@H]3C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 19, 19, 26, 26, 26, 26, 4, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 319) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/319: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](NC(=O)OC(C)(C)C)[C@H]3C2)cc1Cl) `ZINC000760648275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760648275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760648275 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](NC(=O)OC(C)(C)C)[C@H]3C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 17, 17, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760648275 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648275 Building ZINC000760648276 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760648276 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/320 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](NC(=O)OC(C)(C)C)[C@@H]3C2)cc1Cl) `ZINC000760648276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760648276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760648276 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](NC(=O)OC(C)(C)C)[C@@H]3C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 13, 13, 22, 24, 24, 24, 3, 3, 3, 4, 4, 4, 10, 10, 10, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 4] 50 rigid atoms, others: [8, 9, 5, 6, 7] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/321 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](NC(=O)OC(C)(C)C)[C@@H]3C2)cc1Cl) `ZINC000760648276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760648276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760648276 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](NC(=O)OC(C)(C)C)[C@@H]3C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 20, 20, 28, 28, 28, 28, 4, 4, 4, 2, 2, 2, 6, 6, 6, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760648276 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276 Building ZINC000760648276 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760648276 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 320) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/320: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](NC(=O)OC(C)(C)C)[C@@H]3C2)cc1Cl) `ZINC000760648276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760648276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760648276 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](NC(=O)OC(C)(C)C)[C@@H]3C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 13, 13, 22, 24, 24, 24, 3, 3, 3, 4, 4, 4, 10, 10, 10, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 4] 50 rigid atoms, others: [8, 9, 5, 6, 7] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 321) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/321: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](NC(=O)OC(C)(C)C)[C@@H]3C2)cc1Cl) `ZINC000760648276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760648276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760648276 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@@H](NC(=O)OC(C)(C)C)[C@@H]3C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 20, 20, 28, 28, 28, 28, 4, 4, 4, 2, 2, 2, 6, 6, 6, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760648276 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648276 Building ZINC000760648277 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760648277 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/322 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](NC(=O)OC(C)(C)C)[C@H]3C2)cc1Cl) `ZINC000760648277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760648277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760648277 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](NC(=O)OC(C)(C)C)[C@H]3C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 18, 18, 28, 28, 28, 28, 3, 3, 3, 2, 2, 2, 5, 5, 5, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 3, 3, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/323 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](NC(=O)OC(C)(C)C)[C@H]3C2)cc1Cl) `ZINC000760648277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760648277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760648277 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](NC(=O)OC(C)(C)C)[C@H]3C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 15, 15, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760648277 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277 Building ZINC000760648277 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760648277 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 322) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/322: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](NC(=O)OC(C)(C)C)[C@H]3C2)cc1Cl) `ZINC000760648277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760648277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760648277 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](NC(=O)OC(C)(C)C)[C@H]3C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 18, 18, 28, 28, 28, 28, 3, 3, 3, 2, 2, 2, 5, 5, 5, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 3, 3, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 323) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](NC(=O)OC(C)(C)C)[C@H]3C2)cc1Cl) `ZINC000760648277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760648277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760648277 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](NC(=O)OC(C)(C)C)[C@H]3C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 15, 15, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760648277 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760648277 Building ZINC000571079240 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000571079240 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/324 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cnn2ccccc12) `ZINC000571079240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000571079240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000571079240 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cnn2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/325 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cnn2ccccc12) `ZINC000571079240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000571079240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000571079240 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cnn2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 8, 8, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000571079240 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240 Building ZINC000571079240 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000571079240 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 324) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cnn2ccccc12) `ZINC000571079240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000571079240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000571079240 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cnn2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 325) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cnn2ccccc12) `ZINC000571079240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000571079240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000571079240 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cnn2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 8, 8, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000571079240 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571079240 Building ZINC000571456507 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000571456507 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/326 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(CCc1ccc(Cl)cc1)C[C@H](O)C(F)(F)F) `ZINC000571456507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000571456507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000571456507 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(CCc1ccc(Cl)cc1)C[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 4, 4, 10, 17, 20, 26, 26, 20, 20, 26, 26, 10, 22, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5, 17, 17, 20, 20, 26, 26, 26, 26, 22, 22, 90] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 307 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/327 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(CCc1ccc(Cl)cc1)C[C@H](O)C(F)(F)F) `ZINC000571456507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000571456507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000571456507 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(CCc1ccc(Cl)cc1)C[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 5, 5, 9, 22, 25, 29, 29, 25, 25, 29, 29, 9, 17, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5, 5, 5, 5, 22, 22, 25, 25, 29, 29, 29, 29, 17, 17, 69] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 267 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000571456507 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507 Building ZINC000571456507 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000571456507 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 326) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(CCc1ccc(Cl)cc1)C[C@H](O)C(F)(F)F) `ZINC000571456507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000571456507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000571456507 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(CCc1ccc(Cl)cc1)C[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 4, 4, 10, 17, 20, 26, 26, 20, 20, 26, 26, 10, 22, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5, 17, 17, 20, 20, 26, 26, 26, 26, 22, 22, 90] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 307 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 327) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(CCc1ccc(Cl)cc1)C[C@H](O)C(F)(F)F) `ZINC000571456507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000571456507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000571456507 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(CCc1ccc(Cl)cc1)C[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 5, 5, 9, 22, 25, 29, 29, 25, 25, 29, 29, 9, 17, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5, 5, 5, 5, 22, 22, 25, 25, 29, 29, 29, 29, 17, 17, 69] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 267 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000571456507 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456507 Building ZINC000571456508 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000571456508 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/328 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(CCc1ccc(Cl)cc1)C[C@@H](O)C(F)(F)F) `ZINC000571456508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000571456508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000571456508 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(CCc1ccc(Cl)cc1)C[C@@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 3, 3, 7, 22, 24, 33, 33, 24, 26, 33, 33, 7, 20, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 5, 22, 22, 24, 24, 33, 33, 33, 33, 20, 20, 78] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 325 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/329 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(CCc1ccc(Cl)cc1)C[C@@H](O)C(F)(F)F) `ZINC000571456508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000571456508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000571456508 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(CCc1ccc(Cl)cc1)C[C@@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 9, 21, 22, 27, 27, 22, 25, 27, 27, 9, 19, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 21, 21, 22, 22, 27, 27, 27, 27, 19, 19, 66] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 265 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000571456508 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508 Building ZINC000571456508 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000571456508 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 328) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(CCc1ccc(Cl)cc1)C[C@@H](O)C(F)(F)F) `ZINC000571456508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000571456508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000571456508 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(CCc1ccc(Cl)cc1)C[C@@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 3, 3, 7, 22, 24, 33, 33, 24, 26, 33, 33, 7, 20, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 5, 22, 22, 24, 24, 33, 33, 33, 33, 20, 20, 78] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 325 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 329) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/329: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(CCc1ccc(Cl)cc1)C[C@@H](O)C(F)(F)F) `ZINC000571456508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000571456508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000571456508 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(CCc1ccc(Cl)cc1)C[C@@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 9, 21, 22, 27, 27, 22, 25, 27, 27, 9, 19, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 21, 21, 22, 22, 27, 27, 27, 27, 19, 19, 66] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 265 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000571456508 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000571456508 Building ZINC000588621614 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000588621614 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/330 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(N)=O)c(F)c1) `ZINC000588621614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588621614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000588621614 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(N)=O)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 4, 14, 14, 14, 14, 14, 14, 4, 4, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 14, 14, 4, 14, 4, 4, 4, 2, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 49 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/331 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/331' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(N)=O)c(F)c1) `ZINC000588621614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588621614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000588621614 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(N)=O)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 13, 13, 5, 13, 3, 3, 3, 3, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000588621614 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614 Building ZINC000588621614 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000588621614 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 330) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/330: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(N)=O)c(F)c1) `ZINC000588621614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588621614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000588621614 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(N)=O)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 4, 14, 14, 14, 14, 14, 14, 4, 4, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 14, 14, 4, 14, 4, 4, 4, 2, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 49 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 331) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/331: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(N)=O)c(F)c1) `ZINC000588621614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588621614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000588621614 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(N)=O)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 13, 13, 5, 13, 3, 3, 3, 3, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000588621614 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588621614 Building ZINC000588643171 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000588643171 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/332 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)N(C)C) `ZINC000588643171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588643171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000588643171 none CC(C)[C@@H](CN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 3, 3, 2, 1, 2, 4, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 3, 5, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 4, 4, 11, 11, 11, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5] 34 rigid atoms, others: [6, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 64 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/333 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/333' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)N(C)C) `ZINC000588643171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588643171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000588643171 none CC(C)[C@@H](CN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 4, 3, 2, 3, 5, 10, 10, 10, 10, 10, 10, 10, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 5, 5, 10, 10, 10, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8] 39 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 69 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000588643171 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171 Building ZINC000588643171 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000588643171 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 332) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)N(C)C) `ZINC000588643171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588643171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000588643171 none CC(C)[C@@H](CN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 3, 3, 2, 1, 2, 4, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 3, 5, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 4, 4, 11, 11, 11, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5] 34 rigid atoms, others: [6, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 64 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 333) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)N(C)C) `ZINC000588643171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588643171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000588643171 none CC(C)[C@@H](CN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 4, 3, 2, 3, 5, 10, 10, 10, 10, 10, 10, 10, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 5, 5, 10, 10, 10, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8] 39 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 69 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000588643171 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643171 Building ZINC000588643176 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000588643176 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/334 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)N(C)C) `ZINC000588643176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588643176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000588643176 none CC(C)[C@H](CN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 4, 3, 2, 3, 5, 10, 10, 10, 10, 10, 10, 10, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 5, 5, 10, 10, 10, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8] 39 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 69 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/335 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/335' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)N(C)C) `ZINC000588643176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588643176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000588643176 none CC(C)[C@H](CN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 3, 3, 2, 1, 2, 4, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 3, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 4, 4, 9, 9, 9, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6] 34 rigid atoms, others: [6, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 63 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000588643176 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176 Building ZINC000588643176 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000588643176 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 334) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)N(C)C) `ZINC000588643176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588643176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000588643176 none CC(C)[C@H](CN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 4, 3, 2, 3, 5, 10, 10, 10, 10, 10, 10, 10, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 5, 5, 10, 10, 10, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8] 39 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 69 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 335) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)N(C)C) `ZINC000588643176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588643176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000588643176 none CC(C)[C@H](CN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 3, 3, 2, 1, 2, 4, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 3, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 4, 4, 9, 9, 9, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6] 34 rigid atoms, others: [6, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 63 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000588643176 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588643176 Building ZINC000588737747 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000588737747 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/336 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(Oc2cccnc2)c1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000588737747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588737747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000588737747 none Cc1nn(C)c(Oc2cccnc2)c1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 12, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 13, 29, 29, 29, 29, 29, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 2, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/337 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/337' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(Oc2cccnc2)c1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000588737747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588737747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000588737747 none Cc1nn(C)c(Oc2cccnc2)c1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 12, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 14, 31, 31, 31, 31, 31, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000588737747 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747 Building ZINC000588737747 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000588737747 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 336) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(Oc2cccnc2)c1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000588737747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588737747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000588737747 none Cc1nn(C)c(Oc2cccnc2)c1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 12, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 13, 29, 29, 29, 29, 29, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 2, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 337) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(Oc2cccnc2)c1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000588737747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588737747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000588737747 none Cc1nn(C)c(Oc2cccnc2)c1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 12, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 14, 31, 31, 31, 31, 31, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000588737747 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588737747 Building ZINC000588744030 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000588744030 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/338 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@](C)CC1) `ZINC000588744030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588744030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000588744030 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 7, 5, 7, 7, 7, 30, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 3, 7, 7, 7, 7, 23, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 136 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/339 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@](C)CC1) `ZINC000588744030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588744030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000588744030 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 7, 5, 7, 7, 7, 31, 41, 41, 41, 41, 41, 41, 41, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 7, 7, 7, 7, 23, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 131 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/340 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/340' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@@](C)CC1) `ZINC000588744030.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000588744030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000588744030 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 9, 6, 9, 9, 9, 32, 41, 41, 41, 41, 41, 41, 41, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 9, 9, 9, 9, 27, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 136 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/341 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/341' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@@](C)CC1) `ZINC000588744030.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000588744030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000588744030 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 7, 5, 7, 7, 7, 33, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 7, 7, 7, 7, 25, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 121 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000588744030 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 Building ZINC000588744030 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000588744030 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 338) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@](C)CC1) `ZINC000588744030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588744030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000588744030 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 7, 5, 7, 7, 7, 30, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 3, 7, 7, 7, 7, 23, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 136 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 339) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/339: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@](C)CC1) `ZINC000588744030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588744030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000588744030 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 7, 5, 7, 7, 7, 31, 41, 41, 41, 41, 41, 41, 41, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 7, 7, 7, 7, 23, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 131 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 340) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@@](C)CC1) `ZINC000588744030.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000588744030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000588744030 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 9, 6, 9, 9, 9, 32, 41, 41, 41, 41, 41, 41, 41, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 9, 9, 9, 9, 27, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 136 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 341) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@@](C)CC1) `ZINC000588744030.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000588744030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000588744030 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 7, 5, 7, 7, 7, 33, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 7, 7, 7, 7, 25, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 121 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000588744030 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 Building ZINC000588744030 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000588744030 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 338) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@](C)CC1) `ZINC000588744030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588744030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000588744030 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 7, 5, 7, 7, 7, 30, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 3, 7, 7, 7, 7, 23, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 136 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 339) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/339: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@](C)CC1) `ZINC000588744030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588744030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000588744030 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 7, 5, 7, 7, 7, 31, 41, 41, 41, 41, 41, 41, 41, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 7, 7, 7, 7, 23, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 131 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 340) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@@](C)CC1) `ZINC000588744030.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000588744030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000588744030 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 9, 6, 9, 9, 9, 32, 41, 41, 41, 41, 41, 41, 41, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 9, 9, 9, 9, 27, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 136 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 341) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@@](C)CC1) `ZINC000588744030.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000588744030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000588744030 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 7, 5, 7, 7, 7, 33, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 7, 7, 7, 7, 25, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 121 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000588744030 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 Building ZINC000588744030 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000588744030 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 338) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@](C)CC1) `ZINC000588744030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588744030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000588744030 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 7, 5, 7, 7, 7, 30, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 3, 7, 7, 7, 7, 23, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 136 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 339) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/339: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@](C)CC1) `ZINC000588744030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588744030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000588744030 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 7, 5, 7, 7, 7, 31, 41, 41, 41, 41, 41, 41, 41, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 7, 7, 7, 7, 23, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 131 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 340) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@@](C)CC1) `ZINC000588744030.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000588744030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000588744030 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 9, 6, 9, 9, 9, 32, 41, 41, 41, 41, 41, 41, 41, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 9, 9, 9, 9, 27, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 136 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 341) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@@](C)CC1) `ZINC000588744030.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000588744030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000588744030 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 7, 5, 7, 7, 7, 33, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 7, 7, 7, 7, 25, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 121 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000588744030 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588744030 Building ZINC000572107530 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000572107530 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/342 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1cc(Oc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)ccn1) `ZINC000572107530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000572107530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000572107530 none CNC(=O)c1cc(Oc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 22, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 7, 4, 4, 4, 6, 30, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 2, 4, 4, 7, 7, 7, 4, 6, 30, 30] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/343 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1cc(Oc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)ccn1) `ZINC000572107530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000572107530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000572107530 none CNC(=O)c1cc(Oc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 19, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 7, 4, 4, 4, 6, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 2, 4, 4, 7, 7, 7, 4, 6, 27, 27] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000572107530 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530 Building ZINC000572107530 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000572107530 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 342) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/342: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1cc(Oc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)ccn1) `ZINC000572107530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000572107530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000572107530 none CNC(=O)c1cc(Oc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 22, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 7, 4, 4, 4, 6, 30, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 2, 4, 4, 7, 7, 7, 4, 6, 30, 30] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 343) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/343: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1cc(Oc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)ccn1) `ZINC000572107530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000572107530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000572107530 none CNC(=O)c1cc(Oc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 19, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 7, 4, 4, 4, 6, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 2, 4, 4, 7, 7, 7, 4, 6, 27, 27] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000572107530 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000572107530 Building ZINC000588796284 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000588796284 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/344 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1c2ccccc2CC[C@H]1C(=O)Nc1ccccc1C) `ZINC000588796284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588796284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000588796284 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1c2ccccc2CC[C@H]1C(=O)Nc1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 35, 35, 22, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 22, 35, 35, 22, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 119 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/345 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2CC[C@H]1C(=O)Nc1ccccc1C) `ZINC000588796284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588796284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000588796284 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2CC[C@H]1C(=O)Nc1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 31, 31, 31, 50, 50, 31, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 31, 50, 50, 31, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000588796284 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284 Building ZINC000588796284 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000588796284 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 344) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/344: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1c2ccccc2CC[C@H]1C(=O)Nc1ccccc1C) `ZINC000588796284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588796284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000588796284 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1c2ccccc2CC[C@H]1C(=O)Nc1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 35, 35, 22, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 22, 35, 35, 22, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 119 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 345) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2CC[C@H]1C(=O)Nc1ccccc1C) `ZINC000588796284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588796284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000588796284 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2CC[C@H]1C(=O)Nc1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 31, 31, 31, 50, 50, 31, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 31, 50, 50, 31, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000588796284 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796284 Building ZINC000588796289 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000588796289 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/346 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1c2ccccc2CC[C@@H]1C(=O)Nc1ccccc1C) `ZINC000588796289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588796289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000588796289 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1c2ccccc2CC[C@@H]1C(=O)Nc1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 48, 48, 28, 48, 48, 48, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 28, 48, 48, 34, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 167 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/347 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2CC[C@@H]1C(=O)Nc1ccccc1C) `ZINC000588796289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588796289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000588796289 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2CC[C@@H]1C(=O)Nc1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 39, 39, 20, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 20, 39, 39, 23, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 140 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000588796289 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289 Building ZINC000588796289 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000588796289 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 346) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/346: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1c2ccccc2CC[C@@H]1C(=O)Nc1ccccc1C) `ZINC000588796289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588796289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000588796289 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1c2ccccc2CC[C@@H]1C(=O)Nc1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 48, 48, 28, 48, 48, 48, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 28, 48, 48, 34, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 167 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 347) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/347: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2CC[C@@H]1C(=O)Nc1ccccc1C) `ZINC000588796289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588796289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000588796289 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2CC[C@@H]1C(=O)Nc1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 39, 39, 20, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 20, 39, 39, 23, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 140 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000588796289 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000588796289 Building ZINC000589039592 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589039592 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/348 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589039592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589039592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000589039592 none CCN(CC)S(=O)(=O)c1ccc2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 39, 29, 39, 46, 5, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/349 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/349' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589039592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589039592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000589039592 none CCN(CC)S(=O)(=O)c1ccc2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 39, 29, 39, 46, 6, 29, 29, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 3, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589039592 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592 Building ZINC000589039592 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589039592 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 348) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589039592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589039592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000589039592 none CCN(CC)S(=O)(=O)c1ccc2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 39, 29, 39, 46, 5, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 349) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589039592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589039592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000589039592 none CCN(CC)S(=O)(=O)c1ccc2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 39, 29, 39, 46, 6, 29, 29, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 3, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589039592 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589039592 Building ZINC000589048773 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589048773 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/350 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1cccc(Cl)c1Cl)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000589048773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589048773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000589048773 none O=C(c1cccc(Cl)c1Cl)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 16, 1, 16, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 13, 29, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 4, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 13, 13, 50, 50, 50, 13, 13, 13, 13, 2, 2, 2, 2, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/351 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/351' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1cccc(Cl)c1Cl)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000589048773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589048773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000589048773 none O=C(c1cccc(Cl)c1Cl)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 16, 1, 16, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 13, 31, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 4, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13] 50 rigid atoms, others: [34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589048773 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773 Building ZINC000589048773 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589048773 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 350) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1cccc(Cl)c1Cl)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000589048773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589048773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000589048773 none O=C(c1cccc(Cl)c1Cl)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 16, 1, 16, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 13, 29, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 4, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 13, 13, 50, 50, 50, 13, 13, 13, 13, 2, 2, 2, 2, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 351) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1cccc(Cl)c1Cl)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000589048773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589048773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000589048773 none O=C(c1cccc(Cl)c1Cl)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 16, 1, 16, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 13, 31, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 4, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13] 50 rigid atoms, others: [34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589048773 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589048773 Building ZINC000589049795 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589049795 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/352 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C(=O)N2CC(=O)Nc3ccccc32)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589049795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589049795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000589049795 none O=C(Nc1ccc(C(=O)N2CC(=O)Nc3ccccc32)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 5, 2, 4, 45, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 5, 5, 50, 50, 50, 50, 50, 48, 50, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/353 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C(=O)N2CC(=O)Nc3ccccc32)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589049795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589049795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000589049795 none O=C(Nc1ccc(C(=O)N2CC(=O)Nc3ccccc32)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 5, 3, 8, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 5, 5, 50, 50, 50, 50, 50, 50, 50, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589049795 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795 Building ZINC000589049795 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589049795 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 352) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/352: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C(=O)N2CC(=O)Nc3ccccc32)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589049795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589049795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000589049795 none O=C(Nc1ccc(C(=O)N2CC(=O)Nc3ccccc32)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 5, 2, 4, 45, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 5, 5, 50, 50, 50, 50, 50, 48, 50, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 353) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/353: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C(=O)N2CC(=O)Nc3ccccc32)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589049795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589049795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000589049795 none O=C(Nc1ccc(C(=O)N2CC(=O)Nc3ccccc32)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 5, 3, 8, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 5, 5, 50, 50, 50, 50, 50, 50, 50, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589049795 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589049795 Building ZINC000589051548 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000589051548 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/354 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C[N@]2CC[N@](c3ccccn3)CC2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589051548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589051548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589051548 none O=C(Nc1ccc(C[N@]2CC[N@](c3ccccn3)CC2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 2, 21, 37, 37, 37, 37, 50, 50, 50, 50, 50, 37, 37, 4, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 4, 4, 17, 17, 37, 37, 37, 37, 50, 50, 50, 50, 37, 37, 37, 37, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/355 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C[N@]2CC[N@@](c3ccccn3)CC2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589051548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589051548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589051548 none O=C(Nc1ccc(C[N@]2CC[N@@](c3ccccn3)CC2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 20, 36, 36, 36, 36, 50, 50, 50, 50, 50, 36, 36, 4, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 4, 4, 16, 16, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36, 36, 36, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/356 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/356' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C[N@]2CC[N@](c3ccccn3)CC2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589051548.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000589051548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589051548 none O=C(Nc1ccc(C[N@]2CC[N@](c3ccccn3)CC2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 4, 20, 36, 36, 36, 36, 50, 50, 50, 50, 50, 36, 36, 4, 4, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 4, 4, 16, 16, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36, 36, 36, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/357 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/357' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C[N@]2CC[N@@](c3ccccn3)CC2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589051548.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000589051548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589051548 none O=C(Nc1ccc(C[N@]2CC[N@@](c3ccccn3)CC2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 4, 20, 36, 36, 36, 36, 50, 50, 50, 50, 50, 36, 36, 4, 4, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 4, 4, 16, 16, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36, 36, 36, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589051548 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 Building ZINC000589051548 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000589051548 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 354) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/354: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C[N@]2CC[N@](c3ccccn3)CC2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589051548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589051548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589051548 none O=C(Nc1ccc(C[N@]2CC[N@](c3ccccn3)CC2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 2, 21, 37, 37, 37, 37, 50, 50, 50, 50, 50, 37, 37, 4, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 4, 4, 17, 17, 37, 37, 37, 37, 50, 50, 50, 50, 37, 37, 37, 37, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 355) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C[N@]2CC[N@@](c3ccccn3)CC2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589051548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589051548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589051548 none O=C(Nc1ccc(C[N@]2CC[N@@](c3ccccn3)CC2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 20, 36, 36, 36, 36, 50, 50, 50, 50, 50, 36, 36, 4, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 4, 4, 16, 16, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36, 36, 36, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 356) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C[N@]2CC[N@](c3ccccn3)CC2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589051548.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000589051548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589051548 none O=C(Nc1ccc(C[N@]2CC[N@](c3ccccn3)CC2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 4, 20, 36, 36, 36, 36, 50, 50, 50, 50, 50, 36, 36, 4, 4, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 4, 4, 16, 16, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36, 36, 36, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 357) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C[N@]2CC[N@@](c3ccccn3)CC2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589051548.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000589051548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589051548 none O=C(Nc1ccc(C[N@]2CC[N@@](c3ccccn3)CC2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 4, 20, 36, 36, 36, 36, 50, 50, 50, 50, 50, 36, 36, 4, 4, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 4, 4, 16, 16, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36, 36, 36, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589051548 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 Building ZINC000589051548 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000589051548 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 354) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/354: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C[N@]2CC[N@](c3ccccn3)CC2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589051548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589051548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589051548 none O=C(Nc1ccc(C[N@]2CC[N@](c3ccccn3)CC2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 2, 21, 37, 37, 37, 37, 50, 50, 50, 50, 50, 37, 37, 4, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 4, 4, 17, 17, 37, 37, 37, 37, 50, 50, 50, 50, 37, 37, 37, 37, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 355) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C[N@]2CC[N@@](c3ccccn3)CC2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589051548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589051548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589051548 none O=C(Nc1ccc(C[N@]2CC[N@@](c3ccccn3)CC2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 20, 36, 36, 36, 36, 50, 50, 50, 50, 50, 36, 36, 4, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 4, 4, 16, 16, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36, 36, 36, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 356) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C[N@]2CC[N@](c3ccccn3)CC2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589051548.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000589051548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589051548 none O=C(Nc1ccc(C[N@]2CC[N@](c3ccccn3)CC2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 4, 20, 36, 36, 36, 36, 50, 50, 50, 50, 50, 36, 36, 4, 4, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 4, 4, 16, 16, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36, 36, 36, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 357) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C[N@]2CC[N@@](c3ccccn3)CC2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589051548.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000589051548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589051548 none O=C(Nc1ccc(C[N@]2CC[N@@](c3ccccn3)CC2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 4, 20, 36, 36, 36, 36, 50, 50, 50, 50, 50, 36, 36, 4, 4, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 4, 4, 16, 16, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36, 36, 36, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589051548 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 Building ZINC000589051548 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000589051548 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 354) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/354: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C[N@]2CC[N@](c3ccccn3)CC2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589051548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589051548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589051548 none O=C(Nc1ccc(C[N@]2CC[N@](c3ccccn3)CC2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 2, 21, 37, 37, 37, 37, 50, 50, 50, 50, 50, 37, 37, 4, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 4, 4, 17, 17, 37, 37, 37, 37, 50, 50, 50, 50, 37, 37, 37, 37, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 355) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C[N@]2CC[N@@](c3ccccn3)CC2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589051548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589051548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589051548 none O=C(Nc1ccc(C[N@]2CC[N@@](c3ccccn3)CC2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 20, 36, 36, 36, 36, 50, 50, 50, 50, 50, 36, 36, 4, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 4, 4, 16, 16, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36, 36, 36, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 356) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C[N@]2CC[N@](c3ccccn3)CC2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589051548.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000589051548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589051548 none O=C(Nc1ccc(C[N@]2CC[N@](c3ccccn3)CC2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 4, 20, 36, 36, 36, 36, 50, 50, 50, 50, 50, 36, 36, 4, 4, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 4, 4, 16, 16, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36, 36, 36, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 357) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C[N@]2CC[N@@](c3ccccn3)CC2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589051548.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000589051548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589051548 none O=C(Nc1ccc(C[N@]2CC[N@@](c3ccccn3)CC2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 4, 20, 36, 36, 36, 36, 50, 50, 50, 50, 50, 36, 36, 4, 4, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 4, 4, 16, 16, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36, 36, 36, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589051548 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589051548 Building ZINC000589054633 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589054633 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/358 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](c1ccc(C(F)(F)F)cc1)N1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589054633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589054633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000589054633 none O=C(NC[C@H](c1ccc(C(F)(F)F)cc1)N1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 23, 42, 42, 43, 43, 43, 43, 43, 43, 43, 43, 43, 42, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 23, 23, 43, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/359 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](c1ccc(C(F)(F)F)cc1)N1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589054633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589054633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000589054633 none O=C(NC[C@H](c1ccc(C(F)(F)F)cc1)N1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 17, 38, 38, 40, 40, 40, 40, 40, 40, 40, 40, 40, 38, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 40, 40, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 186 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589054633 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633 Building ZINC000589054633 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589054633 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 358) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/358: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](c1ccc(C(F)(F)F)cc1)N1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589054633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589054633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000589054633 none O=C(NC[C@H](c1ccc(C(F)(F)F)cc1)N1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 23, 42, 42, 43, 43, 43, 43, 43, 43, 43, 43, 43, 42, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 23, 23, 43, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 359) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](c1ccc(C(F)(F)F)cc1)N1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589054633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589054633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000589054633 none O=C(NC[C@H](c1ccc(C(F)(F)F)cc1)N1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 17, 38, 38, 40, 40, 40, 40, 40, 40, 40, 40, 40, 38, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 40, 40, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 186 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589054633 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054633 Building ZINC000589054636 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589054636 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/360 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](c1ccc(C(F)(F)F)cc1)N1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589054636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589054636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000589054636 none O=C(NC[C@@H](c1ccc(C(F)(F)F)cc1)N1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 17, 39, 39, 40, 40, 39, 39, 40, 40, 40, 40, 40, 39, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 199 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/361 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/361' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](c1ccc(C(F)(F)F)cc1)N1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589054636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589054636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000589054636 none O=C(NC[C@@H](c1ccc(C(F)(F)F)cc1)N1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 40, 40, 42, 42, 42, 42, 42, 42, 42, 42, 42, 40, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 23, 23, 42, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589054636 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636 Building ZINC000589054636 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589054636 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 360) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](c1ccc(C(F)(F)F)cc1)N1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589054636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589054636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000589054636 none O=C(NC[C@@H](c1ccc(C(F)(F)F)cc1)N1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 17, 39, 39, 40, 40, 39, 39, 40, 40, 40, 40, 40, 39, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 199 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 361) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](c1ccc(C(F)(F)F)cc1)N1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589054636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589054636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000589054636 none O=C(NC[C@@H](c1ccc(C(F)(F)F)cc1)N1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 40, 40, 42, 42, 42, 42, 42, 42, 42, 42, 42, 40, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 23, 23, 42, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589054636 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589054636 Building ZINC000589093980 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589093980 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/362 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2nc(c3ccc(Cl)cc3)no2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589093980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589093980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000589093980 none O=C(N1CCN(Cc2nc(c3ccc(Cl)cc3)no2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 7, 7, 7, 7, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1] 50 rigid atoms, others: [1, 44, 45, 46, 47, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/363 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2nc(c3ccc(Cl)cc3)no2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589093980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589093980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000589093980 none O=C(N1CCN(Cc2nc(c3ccc(Cl)cc3)no2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 5, 5, 5, 5, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 13, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1] 50 rigid atoms, others: [1, 44, 45, 46, 47, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589093980 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980 Building ZINC000589093980 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589093980 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 362) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2nc(c3ccc(Cl)cc3)no2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589093980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589093980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000589093980 none O=C(N1CCN(Cc2nc(c3ccc(Cl)cc3)no2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 7, 7, 7, 7, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1] 50 rigid atoms, others: [1, 44, 45, 46, 47, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 363) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2nc(c3ccc(Cl)cc3)no2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589093980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589093980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000589093980 none O=C(N1CCN(Cc2nc(c3ccc(Cl)cc3)no2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 5, 5, 5, 5, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 13, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1] 50 rigid atoms, others: [1, 44, 45, 46, 47, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589093980 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589093980 Building ZINC000589095302 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589095302 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/364 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2csc(c3ccccc3)n2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589095302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589095302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000589095302 none O=C(N1CCN(Cc2csc(c3ccccc3)n2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 8, 8, 8, 8, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 8, 8, 24, 24, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/365 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2csc(c3ccccc3)n2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589095302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589095302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000589095302 none O=C(N1CCN(Cc2csc(c3ccccc3)n2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 8, 8, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 22, 22, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1] 50 rigid atoms, others: [1, 45, 46, 47, 48, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589095302 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302 Building ZINC000589095302 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589095302 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 364) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2csc(c3ccccc3)n2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589095302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589095302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000589095302 none O=C(N1CCN(Cc2csc(c3ccccc3)n2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 8, 8, 8, 8, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 8, 8, 24, 24, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 365) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2csc(c3ccccc3)n2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589095302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589095302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000589095302 none O=C(N1CCN(Cc2csc(c3ccccc3)n2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 8, 8, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 22, 22, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1] 50 rigid atoms, others: [1, 45, 46, 47, 48, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589095302 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589095302 Building ZINC000589097288 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589097288 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/366 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(c2noc([C@H](C)N3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)cc1) `ZINC000589097288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589097288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589097288 none Cc1ccc(c2noc([C@H](C)N3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 23, 8, 23, 23, 8, 8, 8, 4, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 8, 8, 50, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 123 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/367 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(c2noc([C@H](C)N3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)cc1) `ZINC000589097288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589097288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589097288 none Cc1ccc(c2noc([C@H](C)N3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 20, 6, 20, 20, 6, 6, 6, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50] 50 rigid atoms, others: [44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53]) total number of confs: 112 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589097288 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288 Building ZINC000589097288 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589097288 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 366) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/366: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(c2noc([C@H](C)N3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)cc1) `ZINC000589097288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589097288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589097288 none Cc1ccc(c2noc([C@H](C)N3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 23, 8, 23, 23, 8, 8, 8, 4, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 8, 8, 50, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 123 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 367) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/367: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(c2noc([C@H](C)N3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)cc1) `ZINC000589097288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589097288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589097288 none Cc1ccc(c2noc([C@H](C)N3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 20, 6, 20, 20, 6, 6, 6, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50] 50 rigid atoms, others: [44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53]) total number of confs: 112 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589097288 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097288 Building ZINC000589097289 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589097289 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/368 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(c2noc([C@@H](C)N3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)cc1) `ZINC000589097289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589097289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589097289 none Cc1ccc(c2noc([C@@H](C)N3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 23, 7, 23, 23, 7, 7, 7, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50] 50 rigid atoms, others: [44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53]) total number of confs: 120 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/369 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(c2noc([C@@H](C)N3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)cc1) `ZINC000589097289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589097289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589097289 none Cc1ccc(c2noc([C@@H](C)N3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 18, 7, 18, 18, 7, 7, 7, 3, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 7, 7, 7, 7, 2, 2, 2, 2, 7, 7, 7, 7, 50, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 109 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589097289 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289 Building ZINC000589097289 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589097289 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 368) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/368: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(c2noc([C@@H](C)N3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)cc1) `ZINC000589097289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589097289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589097289 none Cc1ccc(c2noc([C@@H](C)N3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 23, 7, 23, 23, 7, 7, 7, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50] 50 rigid atoms, others: [44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53]) total number of confs: 120 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 369) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/369: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(c2noc([C@@H](C)N3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)cc1) `ZINC000589097289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589097289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000589097289 none Cc1ccc(c2noc([C@@H](C)N3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 18, 7, 18, 18, 7, 7, 7, 3, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 7, 7, 7, 7, 2, 2, 2, 2, 7, 7, 7, 7, 50, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 109 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589097289 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589097289 Building ZINC000589101788 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589101788 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/370 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccc(Cl)cc1Cl)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000589101788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589101788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000589101788 none O=C(c1ccc(Cl)cc1Cl)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 16, 1, 1, 16, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 14, 29, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 4, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 14, 14, 14, 14] 50 rigid atoms, others: [34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/371 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccc(Cl)cc1Cl)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000589101788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589101788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000589101788 none O=C(c1ccc(Cl)cc1Cl)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 16, 1, 1, 16, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 15, 31, 50, 50, 31, 50, 50, 50, 50, 15, 15, 15, 4, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 15, 15, 50, 50, 50, 15, 15, 15, 15, 2, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589101788 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788 Building ZINC000589101788 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589101788 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 370) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccc(Cl)cc1Cl)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000589101788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589101788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000589101788 none O=C(c1ccc(Cl)cc1Cl)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 16, 1, 1, 16, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 14, 29, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 4, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 14, 14, 14, 14] 50 rigid atoms, others: [34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 371) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/371: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccc(Cl)cc1Cl)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000589101788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589101788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000589101788 none O=C(c1ccc(Cl)cc1Cl)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 16, 1, 1, 16, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 15, 31, 50, 50, 31, 50, 50, 50, 50, 15, 15, 15, 4, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 15, 15, 50, 50, 50, 15, 15, 15, 15, 2, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589101788 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589101788 Building ZINC000589111006 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589111006 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/372 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN(Cc1ccc(OCc2ccccc2)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589111006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589111006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000589111006 none NC(=O)CN(Cc1ccc(OCc2ccccc2)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 9, 5, 3, 5, 7, 8, 8, 7, 8, 19, 43, 50, 50, 44, 50, 50, 8, 8, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 8, 8, 7, 7, 8, 8, 43, 43, 50, 50, 43, 50, 50, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 198 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/373 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN(Cc1ccc(OCc2ccccc2)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589111006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589111006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000589111006 none NC(=O)CN(Cc1ccc(OCc2ccccc2)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 9, 5, 3, 5, 7, 8, 8, 7, 7, 19, 43, 50, 50, 43, 50, 50, 8, 8, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 8, 8, 7, 7, 8, 8, 43, 43, 50, 50, 43, 50, 50, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 198 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589111006 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006 Building ZINC000589111006 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589111006 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 372) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/372: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN(Cc1ccc(OCc2ccccc2)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589111006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589111006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000589111006 none NC(=O)CN(Cc1ccc(OCc2ccccc2)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 9, 5, 3, 5, 7, 8, 8, 7, 8, 19, 43, 50, 50, 44, 50, 50, 8, 8, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 8, 8, 7, 7, 8, 8, 43, 43, 50, 50, 43, 50, 50, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 198 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 373) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/373: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN(Cc1ccc(OCc2ccccc2)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589111006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589111006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000589111006 none NC(=O)CN(Cc1ccc(OCc2ccccc2)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 9, 5, 3, 5, 7, 8, 8, 7, 7, 19, 43, 50, 50, 43, 50, 50, 8, 8, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 8, 8, 7, 7, 8, 8, 43, 43, 50, 50, 43, 50, 50, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 198 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589111006 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589111006 Building ZINC000589123450 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589123450 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/374 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1NS(=O)(=O)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589123450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589123450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000589123450 none O=C(NCc1ccccc1NS(=O)(=O)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 19, 26, 26, 26, 26, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 19, 19, 26, 26, 26, 26, 31, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 213 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/375 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/375' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1NS(=O)(=O)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589123450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589123450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000589123450 none O=C(NCc1ccccc1NS(=O)(=O)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 19, 26, 26, 26, 26, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 19, 19, 26, 26, 26, 26, 31, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 213 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589123450 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450 Building ZINC000589123450 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589123450 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 374) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/374: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1NS(=O)(=O)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589123450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589123450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000589123450 none O=C(NCc1ccccc1NS(=O)(=O)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 19, 26, 26, 26, 26, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 19, 19, 26, 26, 26, 26, 31, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 213 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 375) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/375: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1NS(=O)(=O)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589123450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589123450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000589123450 none O=C(NCc1ccccc1NS(=O)(=O)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 19, 26, 26, 26, 26, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 19, 19, 26, 26, 26, 26, 31, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 213 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589123450 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589123450 Building ZINC000589352495 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589352495 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/376 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(CC(=O)N2CCc3ccc(NC(=O)[C@]([O-])([SiH3])c4ccc(C)cc4)cc32)c1) `ZINC000589352495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589352495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000589352495 none COc1cccc(CC(=O)N2CCc3ccc(NC(=O)[C@]([O-])([SiH3])c4ccc(C)cc4)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 32, 21, 12, 21, 12, 12, 12, 12, 12, 12, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 12, 12, 50, 50, 50, 50, 50, 50, 50, 32, 32, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 12, 50] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 140 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/377 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(CC(=O)N2CCc3ccc(NC(=O)[C@@]([O-])([SiH3])c4ccc(C)cc4)cc32)c1) `ZINC000589352495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589352495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000589352495 none COc1cccc(CC(=O)N2CCc3ccc(NC(=O)[C@@]([O-])([SiH3])c4ccc(C)cc4)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 29, 20, 13, 20, 13, 13, 13, 13, 13, 13, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 13, 13, 50, 50, 50, 50, 50, 50, 50, 29, 29, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 13, 50] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 132 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589352495 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495 Building ZINC000589352495 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589352495 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 376) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/376: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(CC(=O)N2CCc3ccc(NC(=O)[C@]([O-])([SiH3])c4ccc(C)cc4)cc32)c1) `ZINC000589352495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589352495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000589352495 none COc1cccc(CC(=O)N2CCc3ccc(NC(=O)[C@]([O-])([SiH3])c4ccc(C)cc4)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 32, 21, 12, 21, 12, 12, 12, 12, 12, 12, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 12, 12, 50, 50, 50, 50, 50, 50, 50, 32, 32, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 12, 50] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 140 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 377) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/377: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(CC(=O)N2CCc3ccc(NC(=O)[C@@]([O-])([SiH3])c4ccc(C)cc4)cc32)c1) `ZINC000589352495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589352495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000589352495 none COc1cccc(CC(=O)N2CCc3ccc(NC(=O)[C@@]([O-])([SiH3])c4ccc(C)cc4)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 29, 20, 13, 20, 13, 13, 13, 13, 13, 13, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 13, 13, 50, 50, 50, 50, 50, 50, 50, 29, 29, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 13, 50] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 132 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589352495 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589352495 Building ZINC000589387982 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589387982 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/378 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1C) `ZINC000589387982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589387982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000589387982 none CCn1nc(C)c(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/379 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1C) `ZINC000589387982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589387982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000589387982 none CCn1nc(C)c(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589387982 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982 Building ZINC000589387982 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589387982 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 378) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/378: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1C) `ZINC000589387982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589387982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000589387982 none CCn1nc(C)c(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 379) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/379: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1C) `ZINC000589387982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589387982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000589387982 none CCn1nc(C)c(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589387982 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589387982 Building ZINC000589935780 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589935780 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/380 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1noc(c2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1) `ZINC000589935780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589935780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000589935780 none CCc1noc(c2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 19, 19, 19, 19, 17, 17, 17, 17, 10, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 17, 17, 19, 29, 29, 29, 29, 29, 17, 17, 10, 10, 7, 7, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 17, 17] 50 rigid atoms, others: [12, 11, 44, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 131 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/381 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1noc(c2ccc(CCNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1) `ZINC000589935780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589935780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000589935780 none CCc1noc(c2ccc(CCNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 20, 20, 20, 20, 19, 19, 19, 19, 10, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 19, 19, 20, 31, 31, 31, 31, 31, 19, 19, 10, 10, 8, 8, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 19, 19] 50 rigid atoms, others: [12, 11, 44, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 132 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589935780 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780 Building ZINC000589935780 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589935780 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 380) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/380: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1noc(c2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1) `ZINC000589935780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589935780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000589935780 none CCc1noc(c2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 19, 19, 19, 19, 17, 17, 17, 17, 10, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 17, 17, 19, 29, 29, 29, 29, 29, 17, 17, 10, 10, 7, 7, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 17, 17] 50 rigid atoms, others: [12, 11, 44, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 131 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 381) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/381: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1noc(c2ccc(CCNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1) `ZINC000589935780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589935780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000589935780 none CCc1noc(c2ccc(CCNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 20, 20, 20, 20, 19, 19, 19, 19, 10, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 19, 19, 20, 31, 31, 31, 31, 31, 19, 19, 10, 10, 8, 8, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 19, 19] 50 rigid atoms, others: [12, 11, 44, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 132 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589935780 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589935780 Building ZINC000590006953 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590006953 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/382 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(Oc2ccccc2)C1) `ZINC000590006953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590006953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000590006953 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(Oc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 13, 13, 11, 13, 13, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 2, 2, 13, 13, 11, 13, 13, 2, 2] 50 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/383 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(Oc2ccccc2)C1) `ZINC000590006953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590006953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000590006953 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(Oc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 11, 11, 10, 11, 11, 2, 2, 2, 2, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 11, 11, 10, 11, 11, 2, 2] 50 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 30 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590006953 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953 Building ZINC000590006953 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590006953 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 382) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/382: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(Oc2ccccc2)C1) `ZINC000590006953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590006953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000590006953 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(Oc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 13, 13, 11, 13, 13, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 2, 2, 13, 13, 11, 13, 13, 2, 2] 50 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 383) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(Oc2ccccc2)C1) `ZINC000590006953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590006953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000590006953 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(Oc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 11, 11, 10, 11, 11, 2, 2, 2, 2, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 11, 11, 10, 11, 11, 2, 2] 50 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 30 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590006953 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590006953 Building ZINC000589977742 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589977742 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/384 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCCN(C)C)C(c1ccccc1)c1ccccc1) `ZINC000589977742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589977742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000589977742 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCCN(C)C)C(c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 9, 17, 19, 29, 30, 30, 9, 21, 22, 22, 21, 22, 22, 21, 22, 22, 21, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 19, 19, 29, 29, 30, 30, 30, 30, 30, 30, 21, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 193 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/385 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCCN(C)C)C(c1ccccc1)c1ccccc1) `ZINC000589977742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589977742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000589977742 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCCN(C)C)C(c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 15, 18, 30, 31, 31, 7, 17, 18, 18, 17, 18, 18, 17, 18, 18, 17, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 18, 18, 30, 30, 31, 31, 31, 31, 31, 31, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 190 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589977742 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742 Building ZINC000589977742 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589977742 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 384) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCCN(C)C)C(c1ccccc1)c1ccccc1) `ZINC000589977742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589977742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000589977742 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCCN(C)C)C(c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 9, 17, 19, 29, 30, 30, 9, 21, 22, 22, 21, 22, 22, 21, 22, 22, 21, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 19, 19, 29, 29, 30, 30, 30, 30, 30, 30, 21, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 193 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 385) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCCN(C)C)C(c1ccccc1)c1ccccc1) `ZINC000589977742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589977742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000589977742 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCCN(C)C)C(c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 15, 18, 30, 31, 31, 7, 17, 18, 18, 17, 18, 18, 17, 18, 18, 17, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 18, 18, 30, 30, 31, 31, 31, 31, 31, 31, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 190 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000589977742 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000589977742 Building ZINC000590116619 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590116619 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/386 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000590116619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590116619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000590116619 none Cc1nn(C)cc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 2, 3, 3, 3, 12, 12, 5, 12, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 53 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/387 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/387' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000590116619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590116619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000590116619 none Cc1nn(C)cc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 49 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590116619 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619 Building ZINC000590116619 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590116619 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 386) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000590116619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590116619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000590116619 none Cc1nn(C)cc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 2, 3, 3, 3, 12, 12, 5, 12, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 53 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 387) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000590116619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590116619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000590116619 none Cc1nn(C)cc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 49 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590116619 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116619 Building ZINC000590116620 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590116620 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/388 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000590116620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590116620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000590116620 none Cc1nn(C)cc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 2, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 53 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/389 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/389' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000590116620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590116620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000590116620 none Cc1nn(C)cc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 2, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 62 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590116620 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620 Building ZINC000590116620 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590116620 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 388) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/388: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000590116620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590116620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000590116620 none Cc1nn(C)cc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 2, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 53 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 389) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/389: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000590116620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590116620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000590116620 none Cc1nn(C)cc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 2, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 62 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590116620 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590116620 Building ZINC000590117027 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590117027 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/390 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](c2ncc[nH]2)C1) `ZINC000590117027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590117027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000590117027 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](c2ncc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 6, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 6, 6, 6, 6, 6, 6, 11, 11, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 68 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/391 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/391' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](c2ncc[nH]2)C1) `ZINC000590117027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590117027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000590117027 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](c2ncc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 4, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 3, 4, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 6, 3, 3, 3, 22, 22, 22, 22, 3, 3, 3, 6, 6, 6, 6, 6, 6, 12, 12, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 90 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590117027 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027 Building ZINC000590117027 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590117027 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 390) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/390: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](c2ncc[nH]2)C1) `ZINC000590117027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590117027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000590117027 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](c2ncc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 6, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 6, 6, 6, 6, 6, 6, 11, 11, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 68 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 391) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/391: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](c2ncc[nH]2)C1) `ZINC000590117027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590117027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000590117027 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](c2ncc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 4, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 3, 4, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 6, 3, 3, 3, 22, 22, 22, 22, 3, 3, 3, 6, 6, 6, 6, 6, 6, 12, 12, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 90 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590117027 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117027 Building ZINC000590117030 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590117030 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/392 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2ncc[nH]2)C1) `ZINC000590117030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590117030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000590117030 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2ncc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 27, 27, 3, 27, 27, 27, 27, 27, 27, 3, 3, 1, 1, 1, 2, 3, 3, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 5, 3, 3, 3, 27, 27, 3, 27, 3, 3, 3, 5, 5, 5, 5, 5, 5, 10, 10, 5, 5] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 78 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/393 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2ncc[nH]2)C1) `ZINC000590117030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590117030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000590117030 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2ncc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 5, 3, 3, 3, 22, 22, 4, 22, 3, 3, 3, 5, 5, 5, 5, 5, 5, 14, 14, 5, 5] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 75 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590117030 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030 Building ZINC000590117030 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590117030 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 392) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/392: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2ncc[nH]2)C1) `ZINC000590117030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590117030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000590117030 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2ncc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 27, 27, 3, 27, 27, 27, 27, 27, 27, 3, 3, 1, 1, 1, 2, 3, 3, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 5, 3, 3, 3, 27, 27, 3, 27, 3, 3, 3, 5, 5, 5, 5, 5, 5, 10, 10, 5, 5] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 78 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 393) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2ncc[nH]2)C1) `ZINC000590117030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590117030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000590117030 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2ncc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 5, 3, 3, 3, 22, 22, 4, 22, 3, 3, 3, 5, 5, 5, 5, 5, 5, 14, 14, 5, 5] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 75 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590117030 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590117030 Building ZINC000590120180 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000590120180 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/394 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1) `ZINC000590120180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590120180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000590120180 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 9, 9, 8, 8, 2, 2, 2, 10, 10, 3, 10, 2, 2, 2, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 49 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/395 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/395' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1) `ZINC000590120180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590120180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000590120180 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 7, 8, 9, 9, 9, 9, 9, 10, 10, 9, 9, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 46 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/396 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/396' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1) `ZINC000590120180.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000590120180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000590120180 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 9, 9, 8, 8, 2, 2, 2, 10, 10, 3, 10, 2, 2, 2, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 49 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/397 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/397' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1) `ZINC000590120180.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000590120180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000590120180 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 7, 8, 9, 9, 9, 9, 9, 10, 10, 9, 9, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 46 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590120180 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 Building ZINC000590120180 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000590120180 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 394) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1) `ZINC000590120180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590120180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000590120180 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 9, 9, 8, 8, 2, 2, 2, 10, 10, 3, 10, 2, 2, 2, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 49 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 395) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1) `ZINC000590120180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590120180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000590120180 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 7, 8, 9, 9, 9, 9, 9, 10, 10, 9, 9, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 46 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 396) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/396: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1) `ZINC000590120180.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000590120180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000590120180 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 9, 9, 8, 8, 2, 2, 2, 10, 10, 3, 10, 2, 2, 2, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 49 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 397) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1) `ZINC000590120180.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000590120180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000590120180 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 7, 8, 9, 9, 9, 9, 9, 10, 10, 9, 9, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 46 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590120180 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 Building ZINC000590120180 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000590120180 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 394) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1) `ZINC000590120180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590120180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000590120180 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 9, 9, 8, 8, 2, 2, 2, 10, 10, 3, 10, 2, 2, 2, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 49 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 395) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1) `ZINC000590120180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590120180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000590120180 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 7, 8, 9, 9, 9, 9, 9, 10, 10, 9, 9, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 46 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 396) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/396: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1) `ZINC000590120180.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000590120180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000590120180 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 9, 9, 8, 8, 2, 2, 2, 10, 10, 3, 10, 2, 2, 2, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 49 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 397) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1) `ZINC000590120180.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000590120180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000590120180 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 7, 8, 9, 9, 9, 9, 9, 10, 10, 9, 9, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 46 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590120180 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 Building ZINC000590120180 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000590120180 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 394) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1) `ZINC000590120180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590120180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000590120180 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 9, 9, 8, 8, 2, 2, 2, 10, 10, 3, 10, 2, 2, 2, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 49 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 395) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1) `ZINC000590120180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590120180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000590120180 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 7, 8, 9, 9, 9, 9, 9, 10, 10, 9, 9, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 46 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 396) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/396: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1) `ZINC000590120180.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000590120180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000590120180 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 9, 9, 8, 8, 2, 2, 2, 10, 10, 3, 10, 2, 2, 2, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 49 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 397) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1) `ZINC000590120180.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000590120180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000590120180 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCN(C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 7, 8, 9, 9, 9, 9, 9, 10, 10, 9, 9, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 46 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590120180 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590120180 Building ZINC000590239033 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590239033 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/398 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2nc3ccccc3n2Cc2cccc(C(F)(F)F)c2)cn1) `ZINC000590239033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590239033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000590239033 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2nc3ccccc3n2Cc2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 32, 32, 12, 32, 32, 32, 32, 32, 32, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 12, 12, 32, 32, 14, 32, 3] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/399 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2nc3ccccc3n2Cc2cccc(C(F)(F)F)c2)cn1) `ZINC000590239033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590239033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000590239033 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2nc3ccccc3n2Cc2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 33, 33, 18, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 13, 13, 33, 33, 15, 33, 3] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590239033 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033 Building ZINC000590239033 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590239033 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 398) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/398: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2nc3ccccc3n2Cc2cccc(C(F)(F)F)c2)cn1) `ZINC000590239033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590239033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000590239033 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2nc3ccccc3n2Cc2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 32, 32, 12, 32, 32, 32, 32, 32, 32, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 12, 12, 32, 32, 14, 32, 3] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 399) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/399: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2nc3ccccc3n2Cc2cccc(C(F)(F)F)c2)cn1) `ZINC000590239033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590239033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000590239033 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2nc3ccccc3n2Cc2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 33, 33, 18, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 13, 13, 33, 33, 15, 33, 3] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590239033 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590239033 Building ZINC000590258005 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590258005 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/400 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1OCc1ccc2ccccc2n1) `ZINC000590258005.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590258005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000590258005 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1OCc1ccc2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 29, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 4, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29, 29, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 6] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/401 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1OCc1ccc2ccccc2n1) `ZINC000590258005.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590258005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000590258005 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1OCc1ccc2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 29, 43, 43, 43, 43, 43, 43, 43, 43, 43, 4, 4, 4, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29, 29, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 6] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590258005 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005 Building ZINC000590258005 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590258005 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 400) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/400: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1OCc1ccc2ccccc2n1) `ZINC000590258005.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590258005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000590258005 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1OCc1ccc2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 29, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 4, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29, 29, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 6] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 401) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/401: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1OCc1ccc2ccccc2n1) `ZINC000590258005.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590258005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000590258005 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1OCc1ccc2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 29, 43, 43, 43, 43, 43, 43, 43, 43, 43, 4, 4, 4, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29, 29, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 6] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590258005 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590258005 Building ZINC000590464485 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590464485 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/402 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(OCCOc2ccc(Cl)cc2)cc1) `ZINC000590464485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590464485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000590464485 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(OCCOc2ccc(Cl)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 7, 7, 5, 7, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 7, 7, 25, 25, 25, 25, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/403 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(OCCOc2ccc(Cl)cc2)cc1) `ZINC000590464485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590464485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000590464485 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(OCCOc2ccc(Cl)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 3, 3, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 26, 26, 26, 26, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590464485 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485 Building ZINC000590464485 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590464485 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 402) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(OCCOc2ccc(Cl)cc2)cc1) `ZINC000590464485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590464485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000590464485 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(OCCOc2ccc(Cl)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 7, 7, 5, 7, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 7, 7, 25, 25, 25, 25, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 403) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(OCCOc2ccc(Cl)cc2)cc1) `ZINC000590464485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590464485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000590464485 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(OCCOc2ccc(Cl)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 3, 3, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 26, 26, 26, 26, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590464485 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590464485 Building ZINC000590678468 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590678468 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/404 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnc(C2CC2)nc1) `ZINC000590678468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590678468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000590678468 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnc(C2CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 21, 21, 4, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 13, 13, 5, 5, 3, 3, 3, 21, 21, 10, 21, 3, 3, 3, 3, 5, 13, 13, 13, 13, 13, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 94 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/405 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/405' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnc(C2CC2)nc1) `ZINC000590678468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590678468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000590678468 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnc(C2CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 11, 11, 5, 5, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 3, 5, 11, 11, 11, 11, 11, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 81 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590678468 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468 Building ZINC000590678468 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590678468 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 404) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnc(C2CC2)nc1) `ZINC000590678468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590678468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000590678468 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnc(C2CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 21, 21, 4, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 13, 13, 5, 5, 3, 3, 3, 21, 21, 10, 21, 3, 3, 3, 3, 5, 13, 13, 13, 13, 13, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 94 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 405) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnc(C2CC2)nc1) `ZINC000590678468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590678468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000590678468 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnc(C2CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 11, 11, 5, 5, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 3, 5, 11, 11, 11, 11, 11, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 81 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590678468 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590678468 Building ZINC000590681845 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590681845 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/406 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nsc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1) `ZINC000590681845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590681845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000590681845 none COc1ccc(c2nsc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 9, 18, 18, 9, 9, 9, 9, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 9, 18, 18, 18, 18, 18, 18, 18, 5, 4, 4, 4, 8, 8, 5, 8, 8, 4, 4, 4, 18, 18] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/407 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nsc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1) `ZINC000590681845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590681845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000590681845 none COc1ccc(c2nsc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 10, 10, 10, 10, 6, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 10, 19, 19, 19, 19, 19, 19, 19, 6, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 19, 19] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590681845 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845 Building ZINC000590681845 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590681845 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 406) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nsc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1) `ZINC000590681845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590681845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000590681845 none COc1ccc(c2nsc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 9, 18, 18, 9, 9, 9, 9, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 9, 18, 18, 18, 18, 18, 18, 18, 5, 4, 4, 4, 8, 8, 5, 8, 8, 4, 4, 4, 18, 18] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 407) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/407: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nsc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1) `ZINC000590681845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590681845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000590681845 none COc1ccc(c2nsc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 10, 10, 10, 10, 6, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 10, 19, 19, 19, 19, 19, 19, 19, 6, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 19, 19] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590681845 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590681845 Building ZINC000590816524 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590816524 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/408 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](n2ccnc2)C1) `ZINC000590816524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590816524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000590816524 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](n2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 2, 2, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 4, 2, 2, 2, 13, 13, 3, 13, 2, 2, 2, 4, 4, 4, 4, 4, 4, 11, 11, 11, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 52 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/409 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/409' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](n2ccnc2)C1) `ZINC000590816524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590816524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000590816524 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](n2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 15, 15, 2, 15, 15, 15, 15, 15, 15, 2, 2, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 4, 2, 2, 2, 15, 15, 2, 15, 2, 2, 2, 4, 4, 4, 4, 4, 4, 12, 12, 12, 4, 4] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 55 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590816524 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524 Building ZINC000590816524 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590816524 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 408) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](n2ccnc2)C1) `ZINC000590816524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590816524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000590816524 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](n2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 2, 2, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 4, 2, 2, 2, 13, 13, 3, 13, 2, 2, 2, 4, 4, 4, 4, 4, 4, 11, 11, 11, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 52 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 409) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](n2ccnc2)C1) `ZINC000590816524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590816524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000590816524 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](n2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 15, 15, 2, 15, 15, 15, 15, 15, 15, 2, 2, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 4, 2, 2, 2, 15, 15, 2, 15, 2, 2, 2, 4, 4, 4, 4, 4, 4, 12, 12, 12, 4, 4] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 55 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590816524 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816524 Building ZINC000590816525 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590816525 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/410 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](n2ccnc2)C1) `ZINC000590816525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590816525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000590816525 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](n2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 14, 14, 2, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 5, 2, 2, 2, 14, 14, 3, 14, 2, 2, 2, 5, 5, 5, 5, 5, 5, 19, 19, 19, 5, 5] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 64 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/411 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](n2ccnc2)C1) `ZINC000590816525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590816525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000590816525 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](n2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 2, 2, 2, 2, 20, 20, 20, 20, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 2, 2] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 37 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590816525 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525 Building ZINC000590816525 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590816525 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 410) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/410: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](n2ccnc2)C1) `ZINC000590816525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590816525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000590816525 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](n2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 14, 14, 2, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 5, 2, 2, 2, 14, 14, 3, 14, 2, 2, 2, 5, 5, 5, 5, 5, 5, 19, 19, 19, 5, 5] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 64 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 411) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/411: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](n2ccnc2)C1) `ZINC000590816525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590816525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000590816525 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](n2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 2, 2, 2, 2, 20, 20, 20, 20, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 2, 2] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 37 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000590816525 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000590816525 Building ZINC000573004826 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000573004826 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/412 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)N(C(=O)Cc2ccccc2)CC3)cn1) `ZINC000573004826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000573004826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000573004826 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)N(C(=O)Cc2ccccc2)CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 6, 10, 10, 20, 20, 32, 32, 32, 32, 32, 32, 10, 10, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 10, 10, 10, 32, 32, 32, 32, 32, 32, 32, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 156 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/413 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)N(C(=O)Cc2ccccc2)CC3)cn1) `ZINC000573004826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000573004826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000573004826 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)N(C(=O)Cc2ccccc2)CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 6, 10, 10, 18, 18, 31, 31, 31, 31, 31, 31, 10, 10, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 10, 10, 10, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 170 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000573004826 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826 Building ZINC000573004826 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000573004826 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 412) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)N(C(=O)Cc2ccccc2)CC3)cn1) `ZINC000573004826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000573004826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000573004826 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)N(C(=O)Cc2ccccc2)CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 6, 10, 10, 20, 20, 32, 32, 32, 32, 32, 32, 10, 10, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 10, 10, 10, 32, 32, 32, 32, 32, 32, 32, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 156 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 413) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)N(C(=O)Cc2ccccc2)CC3)cn1) `ZINC000573004826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000573004826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000573004826 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)N(C(=O)Cc2ccccc2)CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 6, 10, 10, 18, 18, 31, 31, 31, 31, 31, 31, 10, 10, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 10, 10, 10, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 170 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000573004826 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573004826 Building ZINC000591054389 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000591054389 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/414 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCOc1cccc2cccnc21) `ZINC000591054389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000591054389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000591054389 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCOc1cccc2cccnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 9, 16, 33, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 10, 10, 12, 12, 15, 15, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/415 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCOc1cccc2cccnc21) `ZINC000591054389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000591054389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000591054389 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCOc1cccc2cccnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 9, 15, 33, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 10, 10, 12, 12, 14, 14, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000591054389 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389 Building ZINC000591054389 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000591054389 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 414) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCOc1cccc2cccnc21) `ZINC000591054389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000591054389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000591054389 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCOc1cccc2cccnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 9, 16, 33, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 10, 10, 12, 12, 15, 15, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 415) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCOc1cccc2cccnc21) `ZINC000591054389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000591054389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000591054389 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCOc1cccc2cccnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 9, 15, 33, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 10, 10, 12, 12, 14, 14, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000591054389 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591054389 Building ZINC000057914058 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000057914058 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/416 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccc(N(C)C)cc1) `ZINC000057914058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000057914058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000057914058 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccc(N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 13, 30, 30, 44, 44, 44, 44, 44, 44, 44, 44, 44, 30, 40, 40, 30, 30, 42, 42, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 13, 13, 44, 44, 44, 44, 44, 40, 40, 42, 42, 42, 42, 42, 42, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 257 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/417 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/417' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccc(N(C)C)cc1) `ZINC000057914058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000057914058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000057914058 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccc(N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 15, 36, 36, 46, 46, 46, 46, 46, 46, 46, 46, 46, 36, 44, 44, 36, 36, 45, 45, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 15, 15, 46, 46, 46, 46, 46, 44, 44, 45, 45, 45, 45, 45, 45, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000057914058 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058 Building ZINC000057914058 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000057914058 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 416) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccc(N(C)C)cc1) `ZINC000057914058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000057914058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000057914058 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccc(N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 13, 30, 30, 44, 44, 44, 44, 44, 44, 44, 44, 44, 30, 40, 40, 30, 30, 42, 42, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 13, 13, 44, 44, 44, 44, 44, 40, 40, 42, 42, 42, 42, 42, 42, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 257 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 417) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccc(N(C)C)cc1) `ZINC000057914058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000057914058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000057914058 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccc(N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 15, 36, 36, 46, 46, 46, 46, 46, 46, 46, 46, 46, 36, 44, 44, 36, 36, 45, 45, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 15, 15, 46, 46, 46, 46, 46, 44, 44, 45, 45, 45, 45, 45, 45, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000057914058 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914058 Building ZINC000057914062 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000057914062 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/418 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccc(N(C)C)cc1) `ZINC000057914062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000057914062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000057914062 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccc(N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 15, 36, 36, 46, 46, 46, 46, 46, 46, 46, 46, 46, 36, 44, 44, 36, 41, 45, 45, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 15, 15, 46, 46, 46, 46, 46, 44, 44, 45, 45, 45, 45, 45, 45, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/419 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccc(N(C)C)cc1) `ZINC000057914062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000057914062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000057914062 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccc(N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 13, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44, 44, 29, 40, 40, 29, 29, 41, 41, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 13, 13, 44, 44, 44, 44, 44, 40, 40, 41, 41, 41, 41, 41, 41, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 261 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000057914062 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062 Building ZINC000057914062 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000057914062 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 418) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccc(N(C)C)cc1) `ZINC000057914062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000057914062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000057914062 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccc(N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 15, 36, 36, 46, 46, 46, 46, 46, 46, 46, 46, 46, 36, 44, 44, 36, 41, 45, 45, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 15, 15, 46, 46, 46, 46, 46, 44, 44, 45, 45, 45, 45, 45, 45, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 419) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccc(N(C)C)cc1) `ZINC000057914062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000057914062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000057914062 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccc(N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 13, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44, 44, 29, 40, 40, 29, 29, 41, 41, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 13, 13, 44, 44, 44, 44, 44, 40, 40, 41, 41, 41, 41, 41, 41, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 261 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000057914062 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000057914062 Building ZINC000760871327 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760871327 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/420 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCNC(=O)c2ccccc2N(C)C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)cc1) `ZINC000760871327.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760871327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760871327 none COc1ccc(CCNC(=O)c2ccccc2N(C)C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 36, 46, 46, 36, 27, 10, 10, 9, 10, 9, 9, 9, 9, 9, 5, 3, 5, 1, 3, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 36, 36, 27, 27, 10, 9, 9, 9, 9, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 46, 46] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/421 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/421' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCNC(=O)c2ccccc2N(C)C(=O)[C@]([O-])([SiH3])c2ccccc2OC)cc1) `ZINC000760871327.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760871327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760871327 none COc1ccc(CCNC(=O)c2ccccc2N(C)C(=O)[C@]([O-])([SiH3])c2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 35, 46, 46, 35, 26, 10, 10, 9, 10, 9, 9, 8, 9, 9, 5, 3, 5, 1, 3, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 35, 35, 26, 26, 10, 9, 9, 9, 9, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 46, 46] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760871327 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327 Building ZINC000760871327 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760871327 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 420) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCNC(=O)c2ccccc2N(C)C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)cc1) `ZINC000760871327.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760871327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760871327 none COc1ccc(CCNC(=O)c2ccccc2N(C)C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 36, 46, 46, 36, 27, 10, 10, 9, 10, 9, 9, 9, 9, 9, 5, 3, 5, 1, 3, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 36, 36, 27, 27, 10, 9, 9, 9, 9, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 46, 46] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 421) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCNC(=O)c2ccccc2N(C)C(=O)[C@]([O-])([SiH3])c2ccccc2OC)cc1) `ZINC000760871327.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760871327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760871327 none COc1ccc(CCNC(=O)c2ccccc2N(C)C(=O)[C@]([O-])([SiH3])c2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 35, 46, 46, 35, 26, 10, 10, 9, 10, 9, 9, 8, 9, 9, 5, 3, 5, 1, 3, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 35, 35, 26, 26, 10, 9, 9, 9, 9, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 46, 46] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760871327 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871327 Building ZINC000760871777 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760871777 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/422 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H](c3ccccc3Br)C2)cc1Cl) `ZINC000760871777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760871777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000760871777 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H](c3ccccc3Br)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 2, 5, 5, 10, 10, 10, 10, 10, 10, 23, 23, 11, 23, 23, 23, 10, 6, 6, 6, 12, 12, 12, 6, 6, 10, 10, 10, 10, 23, 23, 11, 23, 10, 10, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/423 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCO[C@H](c3ccccc3Br)C2)cc1Cl) `ZINC000760871777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760871777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000760871777 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCO[C@H](c3ccccc3Br)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 2, 5, 5, 9, 9, 9, 9, 9, 9, 20, 20, 9, 20, 20, 20, 9, 6, 6, 6, 12, 12, 12, 6, 6, 9, 9, 9, 9, 20, 20, 9, 20, 9, 9, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760871777 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777 Building ZINC000760871777 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760871777 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 422) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/422: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H](c3ccccc3Br)C2)cc1Cl) `ZINC000760871777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760871777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000760871777 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H](c3ccccc3Br)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 2, 5, 5, 10, 10, 10, 10, 10, 10, 23, 23, 11, 23, 23, 23, 10, 6, 6, 6, 12, 12, 12, 6, 6, 10, 10, 10, 10, 23, 23, 11, 23, 10, 10, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 423) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/423: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCO[C@H](c3ccccc3Br)C2)cc1Cl) `ZINC000760871777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760871777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000760871777 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCO[C@H](c3ccccc3Br)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 2, 5, 5, 9, 9, 9, 9, 9, 9, 20, 20, 9, 20, 20, 20, 9, 6, 6, 6, 12, 12, 12, 6, 6, 9, 9, 9, 9, 20, 20, 9, 20, 9, 9, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760871777 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871777 Building ZINC000760871778 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760871778 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/424 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3ccccc3Br)C2)cc1Cl) `ZINC000760871778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760871778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000760871778 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3ccccc3Br)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 2, 4, 5, 9, 9, 9, 9, 9, 9, 20, 20, 9, 20, 20, 20, 9, 6, 6, 6, 12, 12, 12, 6, 6, 9, 9, 9, 9, 20, 20, 9, 20, 9, 9, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/425 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/425' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3ccccc3Br)C2)cc1Cl) `ZINC000760871778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760871778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000760871778 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3ccccc3Br)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 6, 6, 1, 1, 1, 2, 4, 5, 10, 10, 10, 10, 10, 10, 23, 23, 13, 23, 23, 23, 10, 6, 6, 6, 10, 10, 10, 6, 6, 10, 10, 10, 10, 23, 23, 19, 23, 10, 10, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760871778 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778 Building ZINC000760871778 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760871778 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 424) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3ccccc3Br)C2)cc1Cl) `ZINC000760871778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760871778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000760871778 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3ccccc3Br)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 2, 4, 5, 9, 9, 9, 9, 9, 9, 20, 20, 9, 20, 20, 20, 9, 6, 6, 6, 12, 12, 12, 6, 6, 9, 9, 9, 9, 20, 20, 9, 20, 9, 9, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 425) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3ccccc3Br)C2)cc1Cl) `ZINC000760871778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760871778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000760871778 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3ccccc3Br)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 6, 6, 1, 1, 1, 2, 4, 5, 10, 10, 10, 10, 10, 10, 23, 23, 13, 23, 23, 23, 10, 6, 6, 6, 10, 10, 10, 6, 6, 10, 10, 10, 10, 23, 23, 19, 23, 10, 10, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760871778 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760871778 Building ZINC000591768693 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000591768693 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/426 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(N2CCCC2)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000591768693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000591768693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000591768693 none COC(=O)c1ccc(N2CCCC2)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 7, 21, 7, 7, 7, 7, 7, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 7, 21, 21, 21, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 2, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 76 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/427 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/427' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(N2CCCC2)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000591768693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000591768693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000591768693 none COC(=O)c1ccc(N2CCCC2)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 7, 27, 7, 7, 7, 7, 7, 9, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 7, 27, 27, 27, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 2, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 75 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000591768693 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693 Building ZINC000591768693 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000591768693 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 426) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(N2CCCC2)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000591768693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000591768693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000591768693 none COC(=O)c1ccc(N2CCCC2)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 7, 21, 7, 7, 7, 7, 7, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 7, 21, 21, 21, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 2, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 76 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 427) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(N2CCCC2)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000591768693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000591768693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000591768693 none COC(=O)c1ccc(N2CCCC2)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 7, 27, 7, 7, 7, 7, 7, 9, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 7, 27, 27, 27, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 2, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 75 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000591768693 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591768693 Building ZINC000573671271 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000573671271 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/428 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1=O) `ZINC000573671271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000573671271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000573671271 none Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 46, 46, 47, 47, 47, 46, 46, 46, 46, 46, 6, 46, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 46, 46, 47, 47, 47, 47, 47, 47, 47, 47, 46, 46, 46, 46, 46, 46, 5, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/429 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/429' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)C1=O) `ZINC000573671271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000573671271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000573671271 none Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 7, 48, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 6, 5, 5, 1, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000573671271 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271 Building ZINC000573671271 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000573671271 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 428) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1=O) `ZINC000573671271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000573671271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000573671271 none Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 46, 46, 47, 47, 47, 46, 46, 46, 46, 46, 6, 46, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 46, 46, 47, 47, 47, 47, 47, 47, 47, 47, 46, 46, 46, 46, 46, 46, 5, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 429) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)C1=O) `ZINC000573671271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000573671271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000573671271 none Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 7, 48, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 6, 5, 5, 1, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000573671271 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671271 Building ZINC000573671272 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000573671272 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/430 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1=O) `ZINC000573671272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000573671272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000573671272 none Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 11, 49, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 6, 5, 5, 1, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/431 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/431' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)C1=O) `ZINC000573671272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000573671272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000573671272 none Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 43, 43, 45, 45, 45, 43, 43, 43, 43, 43, 10, 43, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 43, 43, 45, 45, 45, 45, 45, 45, 45, 45, 43, 43, 43, 43, 43, 43, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000573671272 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272 Building ZINC000573671272 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000573671272 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 430) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/430: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1=O) `ZINC000573671272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000573671272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000573671272 none Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 11, 49, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 6, 5, 5, 1, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 431) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/431: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)C1=O) `ZINC000573671272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000573671272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000573671272 none Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 43, 43, 45, 45, 45, 43, 43, 43, 43, 43, 10, 43, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 43, 43, 45, 45, 45, 45, 45, 45, 45, 45, 43, 43, 43, 43, 43, 43, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000573671272 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000573671272 Building ZINC000760903263 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760903263 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/432 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CC[C@H](NC(=O)OC(C)(C)C)C(C)C)cc1Cl) `ZINC000760903263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760903263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000760903263 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CC[C@H](NC(=O)OC(C)(C)C)C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 6, 6, 14, 14, 17, 25, 25, 26, 26, 26, 26, 14, 18, 18, 2, 2, 2, 4, 4, 4, 2, 2, 3, 3, 3, 6, 6, 6, 6, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 18, 18, 18, 18, 18, 18, 18, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/433 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/433' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CC[C@H](NC(=O)OC(C)(C)C)C(C)C)cc1Cl) `ZINC000760903263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760903263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000760903263 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CC[C@H](NC(=O)OC(C)(C)C)C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 6, 6, 12, 12, 15, 23, 23, 26, 26, 26, 26, 12, 17, 17, 2, 2, 2, 5, 5, 5, 2, 2, 3, 3, 3, 6, 6, 6, 6, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 17, 17, 17, 17, 17, 17, 17, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760903263 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263 Building ZINC000760903263 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760903263 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 432) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CC[C@H](NC(=O)OC(C)(C)C)C(C)C)cc1Cl) `ZINC000760903263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760903263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000760903263 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CC[C@H](NC(=O)OC(C)(C)C)C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 6, 6, 14, 14, 17, 25, 25, 26, 26, 26, 26, 14, 18, 18, 2, 2, 2, 4, 4, 4, 2, 2, 3, 3, 3, 6, 6, 6, 6, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 18, 18, 18, 18, 18, 18, 18, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 433) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CC[C@H](NC(=O)OC(C)(C)C)C(C)C)cc1Cl) `ZINC000760903263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760903263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000760903263 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CC[C@H](NC(=O)OC(C)(C)C)C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 6, 6, 12, 12, 15, 23, 23, 26, 26, 26, 26, 12, 17, 17, 2, 2, 2, 5, 5, 5, 2, 2, 3, 3, 3, 6, 6, 6, 6, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 17, 17, 17, 17, 17, 17, 17, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760903263 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903263 Building ZINC000760903264 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760903264 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/434 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CC[C@@H](NC(=O)OC(C)(C)C)C(C)C)cc1Cl) `ZINC000760903264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760903264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000760903264 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CC[C@@H](NC(=O)OC(C)(C)C)C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 5, 5, 10, 10, 13, 20, 20, 24, 24, 24, 24, 10, 15, 15, 2, 2, 2, 5, 5, 5, 2, 2, 3, 3, 3, 5, 5, 5, 5, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 15, 15, 15, 15, 15, 15, 15, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/435 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/435' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CC[C@@H](NC(=O)OC(C)(C)C)C(C)C)cc1Cl) `ZINC000760903264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760903264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000760903264 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CC[C@@H](NC(=O)OC(C)(C)C)C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 7, 7, 16, 16, 19, 26, 26, 29, 29, 29, 29, 16, 21, 21, 2, 2, 2, 4, 4, 4, 2, 2, 3, 3, 3, 7, 7, 7, 7, 19, 29, 29, 29, 29, 29, 29, 29, 29, 29, 21, 21, 21, 21, 21, 21, 21, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760903264 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264 Building ZINC000760903264 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760903264 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 434) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CC[C@@H](NC(=O)OC(C)(C)C)C(C)C)cc1Cl) `ZINC000760903264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760903264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000760903264 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CC[C@@H](NC(=O)OC(C)(C)C)C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 5, 5, 10, 10, 13, 20, 20, 24, 24, 24, 24, 10, 15, 15, 2, 2, 2, 5, 5, 5, 2, 2, 3, 3, 3, 5, 5, 5, 5, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 15, 15, 15, 15, 15, 15, 15, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 435) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/435: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CC[C@@H](NC(=O)OC(C)(C)C)C(C)C)cc1Cl) `ZINC000760903264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760903264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000760903264 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CC[C@@H](NC(=O)OC(C)(C)C)C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 7, 7, 16, 16, 19, 26, 26, 29, 29, 29, 29, 16, 21, 21, 2, 2, 2, 4, 4, 4, 2, 2, 3, 3, 3, 7, 7, 7, 7, 19, 29, 29, 29, 29, 29, 29, 29, 29, 29, 21, 21, 21, 21, 21, 21, 21, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760903264 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760903264 Building ZINC000760902347 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760902347 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/436 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@](O)(c2ccc(Cl)cc2)C(F)(F)F)cc1Cl) `ZINC000760902347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760902347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000760902347 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@](O)(c2ccc(Cl)cc2)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 1, 4, 4, 4, 13, 20, 20, 24, 24, 20, 20, 24, 24, 20, 20, 20, 20, 5, 5, 5, 10, 10, 10, 5, 5, 4, 13, 13, 60, 24, 24, 24, 24, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 185 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/437 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/437' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@](O)(c2ccc(Cl)cc2)C(F)(F)F)cc1Cl) `ZINC000760902347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760902347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000760902347 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@](O)(c2ccc(Cl)cc2)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 22, 22, 23, 23, 22, 22, 23, 23, 22, 22, 22, 22, 6, 6, 6, 13, 13, 13, 6, 6, 2, 11, 11, 66, 23, 23, 23, 23, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 193 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760902347 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347 Building ZINC000760902347 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760902347 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 436) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/436: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@](O)(c2ccc(Cl)cc2)C(F)(F)F)cc1Cl) `ZINC000760902347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760902347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000760902347 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@](O)(c2ccc(Cl)cc2)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 1, 4, 4, 4, 13, 20, 20, 24, 24, 20, 20, 24, 24, 20, 20, 20, 20, 5, 5, 5, 10, 10, 10, 5, 5, 4, 13, 13, 60, 24, 24, 24, 24, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 185 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 437) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@](O)(c2ccc(Cl)cc2)C(F)(F)F)cc1Cl) `ZINC000760902347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760902347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000760902347 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@](O)(c2ccc(Cl)cc2)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 22, 22, 23, 23, 22, 22, 23, 23, 22, 22, 22, 22, 6, 6, 6, 13, 13, 13, 6, 6, 2, 11, 11, 66, 23, 23, 23, 23, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 193 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760902347 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902347 Building ZINC000760902349 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760902349 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/438 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@](O)(c2ccc(Cl)cc2)C(F)(F)F)cc1Cl) `ZINC000760902349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760902349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000760902349 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@](O)(c2ccc(Cl)cc2)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 23, 23, 25, 25, 23, 23, 25, 25, 23, 23, 23, 23, 6, 6, 6, 13, 13, 13, 6, 6, 2, 11, 11, 69, 25, 25, 25, 25, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 207 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/439 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/439' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@](O)(c2ccc(Cl)cc2)C(F)(F)F)cc1Cl) `ZINC000760902349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760902349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000760902349 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@](O)(c2ccc(Cl)cc2)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 13, 20, 20, 24, 24, 20, 20, 24, 24, 20, 20, 20, 20, 5, 5, 5, 10, 10, 10, 5, 5, 4, 13, 13, 60, 24, 24, 24, 24, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 173 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760902349 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349 Building ZINC000760902349 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760902349 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 438) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/438: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@](O)(c2ccc(Cl)cc2)C(F)(F)F)cc1Cl) `ZINC000760902349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760902349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000760902349 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@](O)(c2ccc(Cl)cc2)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 23, 23, 25, 25, 23, 23, 25, 25, 23, 23, 23, 23, 6, 6, 6, 13, 13, 13, 6, 6, 2, 11, 11, 69, 25, 25, 25, 25, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 207 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 439) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/439: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@](O)(c2ccc(Cl)cc2)C(F)(F)F)cc1Cl) `ZINC000760902349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760902349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000760902349 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@](O)(c2ccc(Cl)cc2)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 13, 20, 20, 24, 24, 20, 20, 24, 24, 20, 20, 20, 20, 5, 5, 5, 10, 10, 10, 5, 5, 4, 13, 13, 60, 24, 24, 24, 24, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 173 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760902349 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760902349 Building ZINC000760904648 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000760904648 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/440 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl) `ZINC000760904648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760904648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904648 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 7, 7, 7, 7, 7, 10, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 7, 7, 7, 18, 18, 18, 18, 54, 18, 18, 18, 18, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 130 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/441 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/441' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl) `ZINC000760904648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760904648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904648 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 7, 7, 5, 7, 7, 10, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 7, 5, 7, 18, 18, 18, 18, 54, 18, 18, 18, 18, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 134 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/442 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/442' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl) `ZINC000760904648.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000760904648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904648 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 8, 8, 5, 8, 8, 11, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 8, 5, 8, 20, 20, 20, 20, 60, 20, 20, 20, 20, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/443 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/443' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl) `ZINC000760904648.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000760904648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904648 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 8, 8, 5, 8, 8, 11, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 8, 5, 8, 20, 20, 20, 20, 60, 20, 20, 20, 20, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760904648 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 Building ZINC000760904648 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000760904648 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 440) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/440: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl) `ZINC000760904648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760904648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904648 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 7, 7, 7, 7, 7, 10, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 7, 7, 7, 18, 18, 18, 18, 54, 18, 18, 18, 18, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 130 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 441) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/441: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl) `ZINC000760904648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760904648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904648 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 7, 7, 5, 7, 7, 10, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 7, 5, 7, 18, 18, 18, 18, 54, 18, 18, 18, 18, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 134 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 442) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl) `ZINC000760904648.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000760904648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904648 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 8, 8, 5, 8, 8, 11, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 8, 5, 8, 20, 20, 20, 20, 60, 20, 20, 20, 20, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 443) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl) `ZINC000760904648.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000760904648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904648 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 8, 8, 5, 8, 8, 11, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 8, 5, 8, 20, 20, 20, 20, 60, 20, 20, 20, 20, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760904648 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 Building ZINC000760904648 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000760904648 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 440) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/440: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl) `ZINC000760904648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760904648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904648 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 7, 7, 7, 7, 7, 10, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 7, 7, 7, 18, 18, 18, 18, 54, 18, 18, 18, 18, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 130 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 441) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/441: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl) `ZINC000760904648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760904648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904648 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 7, 7, 5, 7, 7, 10, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 7, 5, 7, 18, 18, 18, 18, 54, 18, 18, 18, 18, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 134 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 442) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl) `ZINC000760904648.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000760904648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904648 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 8, 8, 5, 8, 8, 11, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 8, 5, 8, 20, 20, 20, 20, 60, 20, 20, 20, 20, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 443) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl) `ZINC000760904648.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000760904648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904648 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 8, 8, 5, 8, 8, 11, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 8, 5, 8, 20, 20, 20, 20, 60, 20, 20, 20, 20, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760904648 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 Building ZINC000760904648 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000760904648 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 440) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/440: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl) `ZINC000760904648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760904648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904648 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 7, 7, 7, 7, 7, 10, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 7, 7, 7, 18, 18, 18, 18, 54, 18, 18, 18, 18, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 130 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 441) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/441: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl) `ZINC000760904648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760904648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904648 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 7, 7, 5, 7, 7, 10, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 7, 5, 7, 18, 18, 18, 18, 54, 18, 18, 18, 18, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 134 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 442) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl) `ZINC000760904648.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000760904648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904648 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 8, 8, 5, 8, 8, 11, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 8, 5, 8, 20, 20, 20, 20, 60, 20, 20, 20, 20, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 443) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl) `ZINC000760904648.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000760904648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904648 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 8, 8, 5, 8, 8, 11, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 8, 5, 8, 20, 20, 20, 20, 60, 20, 20, 20, 20, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760904648 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904648 Building ZINC000760904650 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000760904650 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/444 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl) `ZINC000760904650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760904650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904650 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 4, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 8, 8, 5, 8, 8, 11, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 8, 5, 8, 21, 21, 21, 21, 63, 21, 21, 21, 21, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/445 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl) `ZINC000760904650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760904650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904650 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 3, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 8, 8, 5, 8, 8, 11, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 8, 5, 8, 21, 21, 21, 21, 63, 21, 21, 21, 21, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 150 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/446 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/446' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl) `ZINC000760904650.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000760904650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904650 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 7, 7, 5, 7, 7, 11, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 14, 14, 14, 6, 6, 3, 5, 5, 5, 7, 5, 7, 21, 21, 21, 21, 63, 21, 21, 21, 21, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 149 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/447 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/447' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl) `ZINC000760904650.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000760904650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904650 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 7, 7, 5, 7, 7, 11, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 14, 14, 14, 6, 6, 3, 5, 5, 5, 7, 5, 7, 21, 21, 21, 21, 63, 21, 21, 21, 21, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 149 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760904650 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 Building ZINC000760904650 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000760904650 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 444) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/444: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl) `ZINC000760904650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760904650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904650 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 4, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 8, 8, 5, 8, 8, 11, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 8, 5, 8, 21, 21, 21, 21, 63, 21, 21, 21, 21, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 445) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/445: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl) `ZINC000760904650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760904650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904650 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 3, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 8, 8, 5, 8, 8, 11, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 8, 5, 8, 21, 21, 21, 21, 63, 21, 21, 21, 21, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 150 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 446) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl) `ZINC000760904650.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000760904650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904650 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 7, 7, 5, 7, 7, 11, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 14, 14, 14, 6, 6, 3, 5, 5, 5, 7, 5, 7, 21, 21, 21, 21, 63, 21, 21, 21, 21, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 149 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 447) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl) `ZINC000760904650.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000760904650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904650 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 7, 7, 5, 7, 7, 11, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 14, 14, 14, 6, 6, 3, 5, 5, 5, 7, 5, 7, 21, 21, 21, 21, 63, 21, 21, 21, 21, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 149 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760904650 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 Building ZINC000760904650 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000760904650 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 444) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/444: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl) `ZINC000760904650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760904650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904650 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 4, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 8, 8, 5, 8, 8, 11, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 8, 5, 8, 21, 21, 21, 21, 63, 21, 21, 21, 21, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 445) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/445: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl) `ZINC000760904650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760904650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904650 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 3, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 8, 8, 5, 8, 8, 11, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 8, 5, 8, 21, 21, 21, 21, 63, 21, 21, 21, 21, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 150 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 446) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl) `ZINC000760904650.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000760904650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904650 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 7, 7, 5, 7, 7, 11, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 14, 14, 14, 6, 6, 3, 5, 5, 5, 7, 5, 7, 21, 21, 21, 21, 63, 21, 21, 21, 21, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 149 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 447) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl) `ZINC000760904650.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000760904650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904650 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 7, 7, 5, 7, 7, 11, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 14, 14, 14, 6, 6, 3, 5, 5, 5, 7, 5, 7, 21, 21, 21, 21, 63, 21, 21, 21, 21, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 149 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760904650 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 Building ZINC000760904650 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000760904650 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 444) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/444: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl) `ZINC000760904650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760904650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904650 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 4, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 8, 8, 5, 8, 8, 11, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 8, 5, 8, 21, 21, 21, 21, 63, 21, 21, 21, 21, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 445) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/445: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl) `ZINC000760904650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760904650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904650 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 3, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 8, 8, 5, 8, 8, 11, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 12, 12, 12, 6, 6, 3, 5, 5, 5, 8, 5, 8, 21, 21, 21, 21, 63, 21, 21, 21, 21, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 150 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 446) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl) `ZINC000760904650.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000760904650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904650 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 7, 7, 5, 7, 7, 11, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 14, 14, 14, 6, 6, 3, 5, 5, 5, 7, 5, 7, 21, 21, 21, 21, 63, 21, 21, 21, 21, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 149 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 447) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl) `ZINC000760904650.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000760904650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000760904650 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2[N@]2CC[C@@H](O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 7, 7, 5, 7, 7, 11, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 14, 14, 14, 6, 6, 3, 5, 5, 5, 7, 5, 7, 21, 21, 21, 21, 63, 21, 21, 21, 21, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 149 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760904650 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760904650 Building ZINC000760917381 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760917381 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/448 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)c2cccc(OCc3ccccc3)c2)cc1Cl) `ZINC000760917381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760917381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000760917381 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)c2cccc(OCc3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 6, 6, 6, 14, 14, 14, 14, 14, 16, 16, 28, 28, 17, 28, 28, 14, 4, 4, 4, 10, 10, 10, 4, 4, 2, 4, 4, 18, 14, 14, 14, 16, 16, 28, 28, 28, 28, 28, 14, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/449 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](O)c2cccc(OCc3ccccc3)c2)cc1Cl) `ZINC000760917381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760917381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000760917381 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](O)c2cccc(OCc3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 3, 5, 5, 5, 10, 10, 10, 10, 10, 13, 13, 28, 28, 14, 28, 28, 10, 4, 4, 4, 11, 11, 11, 4, 4, 2, 3, 3, 15, 10, 10, 10, 13, 13, 28, 28, 28, 28, 28, 10, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760917381 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381 Building ZINC000760917381 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760917381 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 448) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/448: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)c2cccc(OCc3ccccc3)c2)cc1Cl) `ZINC000760917381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760917381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000760917381 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)c2cccc(OCc3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 6, 6, 6, 14, 14, 14, 14, 14, 16, 16, 28, 28, 17, 28, 28, 14, 4, 4, 4, 10, 10, 10, 4, 4, 2, 4, 4, 18, 14, 14, 14, 16, 16, 28, 28, 28, 28, 28, 14, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 449) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](O)c2cccc(OCc3ccccc3)c2)cc1Cl) `ZINC000760917381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760917381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000760917381 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](O)c2cccc(OCc3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 3, 5, 5, 5, 10, 10, 10, 10, 10, 13, 13, 28, 28, 14, 28, 28, 10, 4, 4, 4, 11, 11, 11, 4, 4, 2, 3, 3, 15, 10, 10, 10, 13, 13, 28, 28, 28, 28, 28, 10, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760917381 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917381 Building ZINC000760917382 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760917382 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/450 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](O)c2cccc(OCc3ccccc3)c2)cc1Cl) `ZINC000760917382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760917382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000760917382 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](O)c2cccc(OCc3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 3, 5, 5, 5, 10, 10, 10, 10, 10, 12, 12, 28, 28, 13, 28, 28, 10, 4, 4, 4, 11, 11, 11, 4, 4, 2, 3, 3, 15, 10, 10, 10, 12, 12, 28, 28, 28, 28, 28, 10, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/451 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/451' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](O)c2cccc(OCc3ccccc3)c2)cc1Cl) `ZINC000760917382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760917382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000760917382 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](O)c2cccc(OCc3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 6, 6, 6, 14, 14, 14, 14, 14, 16, 16, 27, 27, 18, 27, 27, 14, 4, 4, 4, 10, 10, 10, 4, 4, 2, 4, 4, 18, 14, 14, 14, 16, 16, 27, 27, 27, 27, 27, 14, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760917382 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382 Building ZINC000760917382 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760917382 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 450) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](O)c2cccc(OCc3ccccc3)c2)cc1Cl) `ZINC000760917382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760917382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000760917382 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](O)c2cccc(OCc3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 3, 5, 5, 5, 10, 10, 10, 10, 10, 12, 12, 28, 28, 13, 28, 28, 10, 4, 4, 4, 11, 11, 11, 4, 4, 2, 3, 3, 15, 10, 10, 10, 12, 12, 28, 28, 28, 28, 28, 10, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 451) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](O)c2cccc(OCc3ccccc3)c2)cc1Cl) `ZINC000760917382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760917382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000760917382 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](O)c2cccc(OCc3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 6, 6, 6, 14, 14, 14, 14, 14, 16, 16, 27, 27, 18, 27, 27, 14, 4, 4, 4, 10, 10, 10, 4, 4, 2, 4, 4, 18, 14, 14, 14, 16, 16, 27, 27, 27, 27, 27, 14, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760917382 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760917382 Building ZINC000760919239 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760919239 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/452 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNc1ccc(S(=O)(=O)C(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC000760919239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760919239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000760919239 none CCNc1ccc(S(=O)(=O)C(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 9, 9, 9, 6, 9, 9, 13, 13, 13, 20, 20, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 14, 14, 14, 14, 14, 13, 9, 9, 20, 9, 4, 6, 6, 13, 13, 13, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/453 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/453' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNc1ccc(S(=O)(=O)C(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC000760919239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760919239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000760919239 none CCNc1ccc(S(=O)(=O)C(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 9, 9, 9, 6, 9, 9, 13, 13, 13, 20, 20, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 15, 15, 15, 15, 15, 14, 9, 9, 20, 9, 4, 6, 6, 13, 13, 13, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760919239 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239 Building ZINC000760919239 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760919239 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 452) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNc1ccc(S(=O)(=O)C(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC000760919239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760919239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000760919239 none CCNc1ccc(S(=O)(=O)C(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 9, 9, 9, 6, 9, 9, 13, 13, 13, 20, 20, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 14, 14, 14, 14, 14, 13, 9, 9, 20, 9, 4, 6, 6, 13, 13, 13, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 453) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNc1ccc(S(=O)(=O)C(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC000760919239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760919239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000760919239 none CCNc1ccc(S(=O)(=O)C(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 9, 9, 9, 6, 9, 9, 13, 13, 13, 20, 20, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 15, 15, 15, 15, 15, 14, 9, 9, 20, 9, 4, 6, 6, 13, 13, 13, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760919239 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760919239 Building ZINC000591994059 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000591994059 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/454 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1OC) `ZINC000591994059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000591994059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000591994059 none COc1ccc(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 26, 26, 26, 26, 9, 4, 8, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 26, 26, 26, 47, 47, 47, 47, 26, 26, 9, 9, 9, 9, 9, 9, 4, 4, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 26, 47, 47, 47] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 45, 46, 47, 48, 54, 55, 56] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53, 57, 58, 59, 60]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/455 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1OC) `ZINC000591994059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000591994059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000591994059 none COc1ccc(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 26, 26, 26, 26, 9, 4, 9, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 26, 26, 26, 49, 46, 46, 46, 26, 26, 9, 9, 9, 9, 9, 9, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 26, 49, 49, 49] 50 rigid atoms, others: [48, 27, 47, 9, 10, 11, 12, 45, 14, 13, 16, 17, 18, 19, 20, 46, 54, 55, 56, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53, 57, 58, 59, 60]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000591994059 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059 Building ZINC000591994059 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000591994059 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 454) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/454: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1OC) `ZINC000591994059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000591994059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000591994059 none COc1ccc(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 26, 26, 26, 26, 9, 4, 8, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 26, 26, 26, 47, 47, 47, 47, 26, 26, 9, 9, 9, 9, 9, 9, 4, 4, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 26, 47, 47, 47] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 45, 46, 47, 48, 54, 55, 56] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53, 57, 58, 59, 60]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 455) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1OC) `ZINC000591994059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000591994059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000591994059 none COc1ccc(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 26, 26, 26, 26, 9, 4, 9, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 26, 26, 26, 49, 46, 46, 46, 26, 26, 9, 9, 9, 9, 9, 9, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 26, 49, 49, 49] 50 rigid atoms, others: [48, 27, 47, 9, 10, 11, 12, 45, 14, 13, 16, 17, 18, 19, 20, 46, 54, 55, 56, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53, 57, 58, 59, 60]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000591994059 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000591994059 Building ZINC000760932636 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760932636 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/456 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC3(C2)CCN(C(=O)OC(C)(C)C)CC3)cc1Cl) `ZINC000760932636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760932636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760932636 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC3(C2)CCN(C(=O)OC(C)(C)C)CC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 25, 25, 25, 25, 9, 9, 4, 4, 4, 6, 6, 6, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 9, 9, 9, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/457 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC3(C2)CCN(C(=O)OC(C)(C)C)CC3)cc1Cl) `ZINC000760932636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760932636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760932636 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC3(C2)CCN(C(=O)OC(C)(C)C)CC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 25, 25, 25, 25, 7, 7, 4, 4, 4, 6, 6, 6, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 7, 7, 7, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760932636 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636 Building ZINC000760932636 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760932636 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 456) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC3(C2)CCN(C(=O)OC(C)(C)C)CC3)cc1Cl) `ZINC000760932636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760932636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760932636 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC3(C2)CCN(C(=O)OC(C)(C)C)CC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 25, 25, 25, 25, 9, 9, 4, 4, 4, 6, 6, 6, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 9, 9, 9, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 457) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/457: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC3(C2)CCN(C(=O)OC(C)(C)C)CC3)cc1Cl) `ZINC000760932636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760932636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000760932636 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC3(C2)CCN(C(=O)OC(C)(C)C)CC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 25, 25, 25, 25, 7, 7, 4, 4, 4, 6, 6, 6, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 7, 7, 7, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000760932636 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000760932636 Building ZINC000592628135 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000592628135 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/458 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCOc1ccccc1C(F)(F)F) `ZINC000592628135.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000592628135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000592628135 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCOc1ccccc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 13, 27, 44, 44, 33, 44, 44, 44, 44, 44, 44, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 9, 9, 13, 13, 44, 44, 37, 44] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/459 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/459' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCOc1ccccc1C(F)(F)F) `ZINC000592628135.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000592628135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000592628135 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCOc1ccccc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 13, 31, 45, 45, 37, 45, 45, 45, 45, 45, 45, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 9, 9, 13, 13, 45, 45, 40, 45] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000592628135 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135 Building ZINC000592628135 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000592628135 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 458) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/458: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCOc1ccccc1C(F)(F)F) `ZINC000592628135.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000592628135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000592628135 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCOc1ccccc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 13, 27, 44, 44, 33, 44, 44, 44, 44, 44, 44, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 9, 9, 13, 13, 44, 44, 37, 44] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 459) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/459: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCOc1ccccc1C(F)(F)F) `ZINC000592628135.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000592628135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000592628135 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCOc1ccccc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 13, 31, 45, 45, 37, 45, 45, 45, 45, 45, 45, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 9, 9, 13, 13, 45, 45, 40, 45] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000592628135 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592628135 Building ZINC000592877170 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000592877170 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/460 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1) `ZINC000592877170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000592877170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877170 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 10, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 15, 15, 15, 15, 13, 3, 3, 3, 11, 11, 10, 11, 3, 3, 3, 2, 13, 13, 13, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/461 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/461' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1) `ZINC000592877170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000592877170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877170 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 14, 14, 14, 14, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/462 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/462' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1) `ZINC000592877170.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000592877170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877170 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 10, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 15, 15, 15, 15, 13, 3, 3, 3, 11, 11, 10, 11, 3, 3, 3, 2, 13, 13, 13, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/463 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/463' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1) `ZINC000592877170.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000592877170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877170 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 14, 14, 14, 14, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000592877170 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 Building ZINC000592877170 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000592877170 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 460) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1) `ZINC000592877170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000592877170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877170 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 10, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 15, 15, 15, 15, 13, 3, 3, 3, 11, 11, 10, 11, 3, 3, 3, 2, 13, 13, 13, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 461) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1) `ZINC000592877170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000592877170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877170 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 14, 14, 14, 14, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 462) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1) `ZINC000592877170.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000592877170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877170 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 10, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 15, 15, 15, 15, 13, 3, 3, 3, 11, 11, 10, 11, 3, 3, 3, 2, 13, 13, 13, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 463) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1) `ZINC000592877170.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000592877170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877170 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 14, 14, 14, 14, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000592877170 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 Building ZINC000592877170 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000592877170 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 460) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1) `ZINC000592877170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000592877170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877170 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 10, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 15, 15, 15, 15, 13, 3, 3, 3, 11, 11, 10, 11, 3, 3, 3, 2, 13, 13, 13, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 461) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1) `ZINC000592877170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000592877170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877170 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 14, 14, 14, 14, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 462) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1) `ZINC000592877170.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000592877170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877170 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 10, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 15, 15, 15, 15, 13, 3, 3, 3, 11, 11, 10, 11, 3, 3, 3, 2, 13, 13, 13, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 463) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1) `ZINC000592877170.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000592877170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877170 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 14, 14, 14, 14, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000592877170 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 Building ZINC000592877170 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000592877170 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 460) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1) `ZINC000592877170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000592877170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877170 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 10, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 15, 15, 15, 15, 13, 3, 3, 3, 11, 11, 10, 11, 3, 3, 3, 2, 13, 13, 13, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 461) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1) `ZINC000592877170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000592877170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877170 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 14, 14, 14, 14, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 462) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1) `ZINC000592877170.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000592877170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877170 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 10, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 15, 15, 15, 15, 13, 3, 3, 3, 11, 11, 10, 11, 3, 3, 3, 2, 13, 13, 13, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 463) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1) `ZINC000592877170.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000592877170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877170 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 14, 14, 14, 14, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000592877170 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877170 Building ZINC000592877171 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000592877171 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/464 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1) `ZINC000592877171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000592877171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 13, 13, 13, 13, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/465 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/465' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1) `ZINC000592877171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000592877171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 10, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 3, 12, 12, 12, 12, 12, 14, 14, 14, 14, 12, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/466 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/466' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1) `ZINC000592877171.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000592877171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 13, 13, 13, 13, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/467 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/467' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1) `ZINC000592877171.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000592877171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 10, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 3, 12, 12, 12, 12, 12, 14, 14, 14, 14, 12, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000592877171 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 Building ZINC000592877171 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000592877171 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 464) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1) `ZINC000592877171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000592877171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 13, 13, 13, 13, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 465) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1) `ZINC000592877171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000592877171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 10, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 3, 12, 12, 12, 12, 12, 14, 14, 14, 14, 12, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 466) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1) `ZINC000592877171.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000592877171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 13, 13, 13, 13, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 467) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1) `ZINC000592877171.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000592877171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 10, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 3, 12, 12, 12, 12, 12, 14, 14, 14, 14, 12, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000592877171 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 Building ZINC000592877171 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000592877171 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 464) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1) `ZINC000592877171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000592877171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 13, 13, 13, 13, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 465) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1) `ZINC000592877171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000592877171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 10, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 3, 12, 12, 12, 12, 12, 14, 14, 14, 14, 12, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 466) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1) `ZINC000592877171.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000592877171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 13, 13, 13, 13, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 467) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1) `ZINC000592877171.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000592877171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 10, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 3, 12, 12, 12, 12, 12, 14, 14, 14, 14, 12, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000592877171 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 Building ZINC000592877171 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000592877171 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 464) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1) `ZINC000592877171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000592877171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 13, 13, 13, 13, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 465) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1) `ZINC000592877171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000592877171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 10, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 3, 12, 12, 12, 12, 12, 14, 14, 14, 14, 12, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 466) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1) `ZINC000592877171.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000592877171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 13, 13, 13, 13, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 467) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1) `ZINC000592877171.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000592877171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000592877171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 10, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 3, 12, 12, 12, 12, 12, 14, 14, 14, 14, 12, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000592877171 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000592877171 Building ZINC000574315403 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000574315403 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/468 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(F)c(Br)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC000574315403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000574315403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000574315403 none COC(=O)c1cc(F)c(Br)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 15, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 9, 20, 9, 9, 3, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 3, 6, 12, 6, 6, 6, 20, 20, 20, 9, 9, 3, 6, 6, 12, 12, 12, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/469 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/469' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(F)c(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC000574315403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000574315403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000574315403 none COC(=O)c1cc(F)c(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 15, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 9, 19, 9, 9, 5, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 19, 19, 19, 9, 9, 3, 6, 6, 13, 13, 13, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000574315403 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403 Building ZINC000574315403 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000574315403 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 468) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(F)c(Br)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC000574315403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000574315403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000574315403 none COC(=O)c1cc(F)c(Br)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 15, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 9, 20, 9, 9, 3, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 3, 6, 12, 6, 6, 6, 20, 20, 20, 9, 9, 3, 6, 6, 12, 12, 12, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 469) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(F)c(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC000574315403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000574315403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000574315403 none COC(=O)c1cc(F)c(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 15, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 9, 19, 9, 9, 5, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 19, 19, 19, 9, 9, 3, 6, 6, 13, 13, 13, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000574315403 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574315403 Building ZINC000594186145 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000594186145 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/470 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCCCC2)C1) `ZINC000594186145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000594186145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000594186145 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 19, 19, 4, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 7, 13, 13, 13, 13, 12, 5, 3, 3, 3, 19, 19, 12, 19, 3, 3, 3, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/471 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCCCC2)C1) `ZINC000594186145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000594186145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000594186145 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 12, 12, 12, 12, 12, 3, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 56 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000594186145 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145 Building ZINC000594186145 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000594186145 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 470) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCCCC2)C1) `ZINC000594186145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000594186145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000594186145 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 19, 19, 4, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 7, 13, 13, 13, 13, 12, 5, 3, 3, 3, 19, 19, 12, 19, 3, 3, 3, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 471) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCCCC2)C1) `ZINC000594186145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000594186145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000594186145 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 12, 12, 12, 12, 12, 3, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 56 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000594186145 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186145 Building ZINC000594186158 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000594186158 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/472 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCCCC2)C1) `ZINC000594186158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000594186158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000594186158 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 5, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 12, 12, 12, 12, 12, 3, 3, 3, 3, 16, 16, 12, 16, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 70 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/473 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/473' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCCCC2)C1) `ZINC000594186158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000594186158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000594186158 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 19, 19, 3, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 7, 13, 13, 13, 13, 12, 5, 3, 3, 3, 19, 19, 3, 19, 3, 3, 3, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 71 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000594186158 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158 Building ZINC000594186158 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000594186158 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 472) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCCCC2)C1) `ZINC000594186158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000594186158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000594186158 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 5, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 12, 12, 12, 12, 12, 3, 3, 3, 3, 16, 16, 12, 16, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 70 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 473) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCCCC2)C1) `ZINC000594186158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000594186158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000594186158 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 19, 19, 3, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 7, 13, 13, 13, 13, 12, 5, 3, 3, 3, 19, 19, 3, 19, 3, 3, 3, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 71 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000594186158 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000594186158 Building ZINC000574533998 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000574533998 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/474 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1) `ZINC000574533998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000574533998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000574533998 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 39, 39, 32, 30, 3, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 3, 12, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 39, 39, 39, 39, 39, 32, 3, 3, 2] 50 rigid atoms, others: [8, 9, 10, 6, 7] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/475 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1) `ZINC000574533998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000574533998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000574533998 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 39, 39, 32, 30, 3, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 3, 12, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 39, 39, 39, 39, 39, 32, 3, 3, 2] 50 rigid atoms, others: [8, 9, 10, 6, 7] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/476 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/476' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1) `ZINC000574533998.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000574533998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000574533998 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 41, 41, 33, 31, 3, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 3, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 41, 41, 41, 41, 41, 33, 3, 3, 2] 50 rigid atoms, others: [8, 9, 10, 6, 7] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/477 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/477' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1) `ZINC000574533998.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000574533998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000574533998 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 41, 41, 33, 31, 3, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 3, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 41, 41, 41, 41, 41, 33, 3, 3, 2] 50 rigid atoms, others: [8, 9, 10, 6, 7] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000574533998 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 Building ZINC000574533998 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000574533998 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 474) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1) `ZINC000574533998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000574533998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000574533998 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 39, 39, 32, 30, 3, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 3, 12, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 39, 39, 39, 39, 39, 32, 3, 3, 2] 50 rigid atoms, others: [8, 9, 10, 6, 7] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 475) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1) `ZINC000574533998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000574533998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000574533998 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 39, 39, 32, 30, 3, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 3, 12, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 39, 39, 39, 39, 39, 32, 3, 3, 2] 50 rigid atoms, others: [8, 9, 10, 6, 7] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 476) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1) `ZINC000574533998.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000574533998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000574533998 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 41, 41, 33, 31, 3, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 3, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 41, 41, 41, 41, 41, 33, 3, 3, 2] 50 rigid atoms, others: [8, 9, 10, 6, 7] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 477) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1) `ZINC000574533998.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000574533998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000574533998 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 41, 41, 33, 31, 3, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 3, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 41, 41, 41, 41, 41, 33, 3, 3, 2] 50 rigid atoms, others: [8, 9, 10, 6, 7] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000574533998 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 Building ZINC000574533998 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000574533998 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 474) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1) `ZINC000574533998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000574533998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000574533998 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 39, 39, 32, 30, 3, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 3, 12, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 39, 39, 39, 39, 39, 32, 3, 3, 2] 50 rigid atoms, others: [8, 9, 10, 6, 7] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 475) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1) `ZINC000574533998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000574533998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000574533998 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 39, 39, 32, 30, 3, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 3, 12, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 39, 39, 39, 39, 39, 32, 3, 3, 2] 50 rigid atoms, others: [8, 9, 10, 6, 7] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 476) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1) `ZINC000574533998.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000574533998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000574533998 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 41, 41, 33, 31, 3, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 3, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 41, 41, 41, 41, 41, 33, 3, 3, 2] 50 rigid atoms, others: [8, 9, 10, 6, 7] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 477) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1) `ZINC000574533998.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000574533998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000574533998 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 41, 41, 33, 31, 3, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 3, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 41, 41, 41, 41, 41, 33, 3, 3, 2] 50 rigid atoms, others: [8, 9, 10, 6, 7] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000574533998 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 Building ZINC000574533998 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000574533998 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 474) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1) `ZINC000574533998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000574533998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000574533998 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 39, 39, 32, 30, 3, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 3, 12, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 39, 39, 39, 39, 39, 32, 3, 3, 2] 50 rigid atoms, others: [8, 9, 10, 6, 7] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 475) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1) `ZINC000574533998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000574533998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000574533998 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 39, 39, 32, 30, 3, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 3, 12, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 39, 39, 39, 39, 39, 32, 3, 3, 2] 50 rigid atoms, others: [8, 9, 10, 6, 7] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 476) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1) `ZINC000574533998.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000574533998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000574533998 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 41, 41, 33, 31, 3, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 3, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 41, 41, 41, 41, 41, 33, 3, 3, 2] 50 rigid atoms, others: [8, 9, 10, 6, 7] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 477) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1) `ZINC000574533998.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000574533998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000574533998 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(CN3CC(C)(C)c4ccc(C5CC5)cc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 41, 41, 33, 31, 3, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 3, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 41, 41, 41, 41, 41, 33, 3, 3, 2] 50 rigid atoms, others: [8, 9, 10, 6, 7] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000574533998 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574533998 Building ZINC000574710543 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000574710543 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/478 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000574710543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000574710543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000574710543 none CC[N@]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 11, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 1, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 16, 16, 16, 16] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 43, 44, 45, 46, 51, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 54, 55, 56, 57]) total number of confs: 51 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/479 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/479' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000574710543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000574710543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000574710543 none CC[N@]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 11, 16, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 5, 5, 5, 5, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 1, 2, 2, 2, 5, 5, 2, 5, 2, 2, 2, 16, 16, 16, 16] 50 rigid atoms, others: [11, 7, 8, 9, 10, 43, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 53 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/480 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/480' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000574710543.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000574710543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000574710543 none CC[N@]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 10, 14, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 1, 2, 2, 2, 7, 7, 2, 7, 2, 2, 2, 14, 14, 14, 14] 50 rigid atoms, others: [11, 7, 8, 9, 10, 43, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 57 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/481 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/481' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000574710543.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000574710543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000574710543 none CC[N@]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 10, 15, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 6, 6, 6, 6, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 1, 2, 2, 2, 6, 6, 2, 6, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [11, 7, 8, 9, 10, 43, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 59 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000574710543 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 Building ZINC000574710543 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000574710543 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 478) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000574710543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000574710543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000574710543 none CC[N@]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 11, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 1, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 16, 16, 16, 16] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 43, 44, 45, 46, 51, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 54, 55, 56, 57]) total number of confs: 51 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 479) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000574710543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000574710543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000574710543 none CC[N@]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 11, 16, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 5, 5, 5, 5, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 1, 2, 2, 2, 5, 5, 2, 5, 2, 2, 2, 16, 16, 16, 16] 50 rigid atoms, others: [11, 7, 8, 9, 10, 43, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 53 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 480) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000574710543.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000574710543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000574710543 none CC[N@]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 10, 14, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 1, 2, 2, 2, 7, 7, 2, 7, 2, 2, 2, 14, 14, 14, 14] 50 rigid atoms, others: [11, 7, 8, 9, 10, 43, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 57 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 481) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000574710543.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000574710543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000574710543 none CC[N@]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 10, 15, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 6, 6, 6, 6, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 1, 2, 2, 2, 6, 6, 2, 6, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [11, 7, 8, 9, 10, 43, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 59 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000574710543 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 Building ZINC000574710543 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000574710543 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 478) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000574710543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000574710543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000574710543 none CC[N@]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 11, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 1, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 16, 16, 16, 16] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 43, 44, 45, 46, 51, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 54, 55, 56, 57]) total number of confs: 51 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 479) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000574710543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000574710543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000574710543 none CC[N@]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 11, 16, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 5, 5, 5, 5, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 1, 2, 2, 2, 5, 5, 2, 5, 2, 2, 2, 16, 16, 16, 16] 50 rigid atoms, others: [11, 7, 8, 9, 10, 43, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 53 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 480) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000574710543.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000574710543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000574710543 none CC[N@]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 10, 14, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 1, 2, 2, 2, 7, 7, 2, 7, 2, 2, 2, 14, 14, 14, 14] 50 rigid atoms, others: [11, 7, 8, 9, 10, 43, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 57 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 481) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000574710543.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000574710543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000574710543 none CC[N@]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 10, 15, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 6, 6, 6, 6, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 1, 2, 2, 2, 6, 6, 2, 6, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [11, 7, 8, 9, 10, 43, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 59 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000574710543 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 Building ZINC000574710543 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000574710543 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 478) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000574710543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000574710543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000574710543 none CC[N@]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 11, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 1, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 16, 16, 16, 16] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 43, 44, 45, 46, 51, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 54, 55, 56, 57]) total number of confs: 51 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 479) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000574710543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000574710543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000574710543 none CC[N@]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 11, 16, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 5, 5, 5, 5, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 1, 2, 2, 2, 5, 5, 2, 5, 2, 2, 2, 16, 16, 16, 16] 50 rigid atoms, others: [11, 7, 8, 9, 10, 43, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 53 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 480) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000574710543.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000574710543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000574710543 none CC[N@]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 10, 14, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 1, 2, 2, 2, 7, 7, 2, 7, 2, 2, 2, 14, 14, 14, 14] 50 rigid atoms, others: [11, 7, 8, 9, 10, 43, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 57 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 481) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000574710543.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000574710543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000574710543 none CC[N@]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 10, 15, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 6, 6, 6, 6, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 1, 2, 2, 2, 6, 6, 2, 6, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [11, 7, 8, 9, 10, 43, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 59 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000574710543 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000574710543 Building ZINC000596017463 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000596017463 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/482 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2nnc3n2CCCC3)cc1) `ZINC000596017463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000596017463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000596017463 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2nnc3n2CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 4, 4, 4, 10, 10, 4, 8, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 4, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 91 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/483 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2nnc3n2CCCC3)cc1) `ZINC000596017463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000596017463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000596017463 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2nnc3n2CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 4, 4, 4, 9, 9, 4, 4, 31, 32, 33, 31, 31, 33, 33, 33, 9, 9, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 4, 9, 9, 31, 31, 33, 33, 33, 33, 33, 33, 9, 9] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 88 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000596017463 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463 Building ZINC000596017463 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000596017463 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 482) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2nnc3n2CCCC3)cc1) `ZINC000596017463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000596017463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000596017463 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2nnc3n2CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 4, 4, 4, 10, 10, 4, 8, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 4, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 91 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 483) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2nnc3n2CCCC3)cc1) `ZINC000596017463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000596017463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000596017463 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2nnc3n2CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 4, 4, 4, 9, 9, 4, 4, 31, 32, 33, 31, 31, 33, 33, 33, 9, 9, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 4, 9, 9, 31, 31, 33, 33, 33, 33, 33, 33, 9, 9] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 88 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000596017463 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000596017463 Building ZINC000597020957 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000597020957 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/484 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccc(F)cc2)C1) `ZINC000597020957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000597020957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000597020957 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 23, 38, 38, 29, 34, 38, 38, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 20, 23, 38, 38, 38, 38, 4, 4] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/485 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/485' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccc(F)cc2)C1) `ZINC000597020957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000597020957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000597020957 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 21, 32, 32, 21, 32, 32, 32, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 18, 21, 32, 32, 32, 32, 4, 4] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000597020957 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957 Building ZINC000597020957 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000597020957 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 484) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccc(F)cc2)C1) `ZINC000597020957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000597020957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000597020957 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 23, 38, 38, 29, 34, 38, 38, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 20, 23, 38, 38, 38, 38, 4, 4] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 485) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccc(F)cc2)C1) `ZINC000597020957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000597020957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000597020957 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 21, 32, 32, 21, 32, 32, 32, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 18, 21, 32, 32, 32, 32, 4, 4] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000597020957 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597020957 Building ZINC000597575080 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000597575080 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/486 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CCOC)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000597575080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000597575080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000597575080 none CCCCN(CCOC)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 12, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 6, 2, 2, 2, 3, 4, 6, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 3, 3, 4, 4, 6, 6, 6, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 61 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/487 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/487' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CCOC)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000597575080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000597575080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000597575080 none CCCCN(CCOC)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 12, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 6, 2, 2, 2, 3, 4, 6, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 3, 3, 4, 4, 6, 6, 6, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 61 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000597575080 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080 Building ZINC000597575080 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000597575080 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 486) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CCOC)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000597575080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000597575080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000597575080 none CCCCN(CCOC)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 12, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 6, 2, 2, 2, 3, 4, 6, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 3, 3, 4, 4, 6, 6, 6, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 61 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 487) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CCOC)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000597575080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000597575080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000597575080 none CCCCN(CCOC)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 12, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 6, 2, 2, 2, 3, 4, 6, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 3, 3, 4, 4, 6, 6, 6, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 61 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000597575080 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597575080 Building ZINC000597587947 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000597587947 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/488 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1nc(c2ccc(Cl)cc2)no1) `ZINC000597587947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000597587947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000597587947 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1nc(c2ccc(Cl)cc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 9, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 8, 8, 9, 9, 40, 40, 40, 40] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/489 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1nc(c2ccc(Cl)cc2)no1) `ZINC000597587947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000597587947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000597587947 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1nc(c2ccc(Cl)cc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 9, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 8, 8, 9, 9, 42, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000597587947 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947 Building ZINC000597587947 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000597587947 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 488) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1nc(c2ccc(Cl)cc2)no1) `ZINC000597587947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000597587947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000597587947 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1nc(c2ccc(Cl)cc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 9, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 8, 8, 9, 9, 40, 40, 40, 40] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 489) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1nc(c2ccc(Cl)cc2)no1) `ZINC000597587947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000597587947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000597587947 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1nc(c2ccc(Cl)cc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 9, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 8, 8, 9, 9, 42, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000597587947 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597587947 Building ZINC000597629997 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000597629997 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/490 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC[C@H]2c2ccccc2)cc1) `ZINC000597629997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000597629997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000597629997 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC[C@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 9, 4, 11, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 9, 9, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 9, 9] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/491 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC[C@H]2c2ccccc2)cc1) `ZINC000597629997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000597629997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000597629997 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC[C@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 5, 30, 30, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 8, 8] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000597629997 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997 Building ZINC000597629997 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000597629997 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 490) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC[C@H]2c2ccccc2)cc1) `ZINC000597629997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000597629997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000597629997 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC[C@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 9, 4, 11, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 9, 9, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 9, 9] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 491) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/491: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC[C@H]2c2ccccc2)cc1) `ZINC000597629997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000597629997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000597629997 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC[C@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 5, 30, 30, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 8, 8] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000597629997 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629997 Building ZINC000597629998 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000597629998 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/492 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC[C@@H]2c2ccccc2)cc1) `ZINC000597629998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000597629998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000597629998 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC[C@@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 13, 33, 33, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 7, 7] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/493 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/493' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC[C@@H]2c2ccccc2)cc1) `ZINC000597629998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000597629998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000597629998 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC[C@@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 2, 9, 32, 32, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 7, 7] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000597629998 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998 Building ZINC000597629998 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000597629998 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 492) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC[C@@H]2c2ccccc2)cc1) `ZINC000597629998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000597629998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000597629998 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC[C@@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 13, 33, 33, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 7, 7] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 493) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC[C@@H]2c2ccccc2)cc1) `ZINC000597629998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000597629998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000597629998 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC[C@@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 2, 9, 32, 32, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 7, 7] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000597629998 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597629998 Building ZINC000597825976 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000597825976 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/494 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)c1ccc(Oc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)cc1) `ZINC000597825976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000597825976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000597825976 none NS(=O)(=O)c1ccc(Oc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)cc1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 50, 42, 42, 42, 27, 4, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 42, 42, 50, 50, 42, 42, 9, 9, 2, 2, 2, 2, 2, 9, 9, 42, 42] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/495 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)c1ccc(Oc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)cc1) `ZINC000597825976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000597825976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000597825976 none NS(=O)(=O)c1ccc(Oc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)cc1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 50, 37, 42, 42, 26, 9, 8, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 42, 42, 50, 50, 42, 42, 9, 9, 2, 2, 2, 2, 2, 9, 9, 42, 42] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000597825976 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976 Building ZINC000597825976 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000597825976 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 494) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)c1ccc(Oc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)cc1) `ZINC000597825976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000597825976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000597825976 none NS(=O)(=O)c1ccc(Oc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)cc1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 50, 42, 42, 42, 27, 4, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 42, 42, 50, 50, 42, 42, 9, 9, 2, 2, 2, 2, 2, 9, 9, 42, 42] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 495) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/495: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)c1ccc(Oc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)cc1) `ZINC000597825976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000597825976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000597825976 none NS(=O)(=O)c1ccc(Oc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)cc1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 50, 37, 42, 42, 26, 9, 8, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 42, 42, 50, 50, 42, 42, 9, 9, 2, 2, 2, 2, 2, 9, 9, 42, 42] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000597825976 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000597825976 Building ZINC000603601039 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603601039 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/496 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2)nc1C) `ZINC000603601039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603601039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000603601039 none CCOC(=O)c1sc(N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 30, 30, 12, 30, 12, 12, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 5, 10, 10, 12, 12, 12, 32, 32, 32, 32, 32, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 5, 10, 10, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/497 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2)nc1C) `ZINC000603601039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603601039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000603601039 none CCOC(=O)c1sc(N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 26, 10, 26, 10, 10, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 11, 11, 7, 11, 11, 10, 10, 10, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 8, 11, 11, 10, 10, 10] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603601039 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039 Building ZINC000603601039 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603601039 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 496) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/496: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2)nc1C) `ZINC000603601039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603601039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000603601039 none CCOC(=O)c1sc(N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 30, 30, 12, 30, 12, 12, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 5, 10, 10, 12, 12, 12, 32, 32, 32, 32, 32, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 5, 10, 10, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 497) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/497: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2)nc1C) `ZINC000603601039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603601039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000603601039 none CCOC(=O)c1sc(N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 26, 10, 26, 10, 10, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 11, 11, 7, 11, 11, 10, 10, 10, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 8, 11, 11, 10, 10, 10] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603601039 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603601039 Building ZINC000603652117 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603652117 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/498 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1nc2ccccc2s1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1) `ZINC000603652117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603652117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000603652117 none C[C@@H](c1nc2ccccc2s1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 14, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 7, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 7, 7, 16, 16, 16, 31, 31, 31, 31, 7, 7, 7, 7, 6, 8, 8, 6, 8, 8, 6, 7, 7, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 91 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/499 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1nc2ccccc2s1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1) `ZINC000603652117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603652117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000603652117 none C[C@@H](c1nc2ccccc2s1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 14, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 9, 22, 22, 35, 35, 35, 35, 35, 35, 35, 35, 9, 9, 9, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 9, 9, 22, 22, 22, 35, 35, 35, 35, 9, 9, 9, 9, 6, 7, 7, 6, 7, 7, 6, 9, 9, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 100 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603652117 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117 Building ZINC000603652117 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603652117 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 498) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/498: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1nc2ccccc2s1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1) `ZINC000603652117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603652117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000603652117 none C[C@@H](c1nc2ccccc2s1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 14, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 7, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 7, 7, 16, 16, 16, 31, 31, 31, 31, 7, 7, 7, 7, 6, 8, 8, 6, 8, 8, 6, 7, 7, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 91 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 499) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1nc2ccccc2s1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1) `ZINC000603652117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603652117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000603652117 none C[C@@H](c1nc2ccccc2s1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 14, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 9, 22, 22, 35, 35, 35, 35, 35, 35, 35, 35, 9, 9, 9, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 9, 9, 22, 22, 22, 35, 35, 35, 35, 9, 9, 9, 9, 6, 7, 7, 6, 7, 7, 6, 9, 9, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 100 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603652117 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652117 Building ZINC000603652118 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603652118 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/500 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1nc2ccccc2s1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1) `ZINC000603652118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603652118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000603652118 none C[C@H](c1nc2ccccc2s1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 14, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 15, 15, 15, 32, 32, 32, 32, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 80 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/501 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1nc2ccccc2s1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1) `ZINC000603652118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603652118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000603652118 none C[C@H](c1nc2ccccc2s1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 14, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 7, 21, 21, 33, 33, 33, 33, 33, 33, 33, 33, 7, 7, 7, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 21, 21, 21, 33, 33, 33, 33, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 97 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603652118 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118 Building ZINC000603652118 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603652118 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 500) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/500: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1nc2ccccc2s1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1) `ZINC000603652118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603652118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000603652118 none C[C@H](c1nc2ccccc2s1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 14, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 15, 15, 15, 32, 32, 32, 32, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 80 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 501) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/501: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1nc2ccccc2s1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1) `ZINC000603652118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603652118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000603652118 none C[C@H](c1nc2ccccc2s1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 14, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 7, 21, 21, 33, 33, 33, 33, 33, 33, 33, 33, 7, 7, 7, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 21, 21, 21, 33, 33, 33, 33, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 97 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603652118 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603652118 Building ZINC000603651825 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000603651825 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/502 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603651825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603651825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000603651825 none O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 8, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 16, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/503 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/503' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603651825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603651825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000603651825 none O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 8, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 16, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/504 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/504' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603651825.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000603651825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000603651825 none O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 8, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 16, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/505 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/505' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603651825.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000603651825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000603651825 none O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 8, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 16, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603651825 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 Building ZINC000603651825 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000603651825 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 502) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603651825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603651825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000603651825 none O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 8, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 16, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 503) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603651825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603651825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000603651825 none O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 8, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 16, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 504) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603651825.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000603651825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000603651825 none O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 8, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 16, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 505) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603651825.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000603651825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000603651825 none O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 8, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 16, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603651825 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 Building ZINC000603651825 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000603651825 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 502) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603651825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603651825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000603651825 none O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 8, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 16, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 503) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603651825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603651825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000603651825 none O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 8, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 16, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 504) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603651825.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000603651825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000603651825 none O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 8, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 16, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 505) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603651825.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000603651825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000603651825 none O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 8, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 16, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603651825 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 Building ZINC000603651825 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000603651825 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 502) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603651825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603651825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000603651825 none O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 8, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 16, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 503) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603651825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603651825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000603651825 none O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 8, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 16, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 504) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603651825.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000603651825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000603651825 none O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 8, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 16, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 505) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603651825.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000603651825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000603651825 none O=C(Nc1ccc(N2CCc3sccc3C2)nc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 8, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 16, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603651825 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603651825 Building ZINC000603653033 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603653033 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/506 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(OCc2cccnc2)cc1) `ZINC000603653033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603653033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000603653033 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(OCc2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 5, 5, 4, 4, 8, 8, 35, 35, 35, 35, 35, 5, 5, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 35, 35, 35, 35, 5, 5] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/507 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(OCc2cccnc2)cc1) `ZINC000603653033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603653033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000603653033 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(OCc2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 5, 5, 4, 4, 8, 8, 39, 39, 39, 39, 39, 5, 5, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 39, 39, 39, 39, 5, 5] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603653033 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033 Building ZINC000603653033 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603653033 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 506) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(OCc2cccnc2)cc1) `ZINC000603653033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603653033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000603653033 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(OCc2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 5, 5, 4, 4, 8, 8, 35, 35, 35, 35, 35, 5, 5, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 35, 35, 35, 35, 5, 5] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 507) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(OCc2cccnc2)cc1) `ZINC000603653033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603653033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000603653033 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(OCc2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 5, 5, 4, 4, 8, 8, 39, 39, 39, 39, 39, 5, 5, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 39, 39, 39, 39, 5, 5] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603653033 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653033 Building ZINC000603653035 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603653035 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/508 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(OCc2cccnc2)cc1) `ZINC000603653035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603653035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000603653035 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(OCc2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 5, 5, 4, 4, 8, 8, 41, 41, 41, 41, 41, 5, 5, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 41, 41, 41, 41, 5, 5] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/509 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/509' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(OCc2cccnc2)cc1) `ZINC000603653035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603653035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000603653035 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(OCc2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 5, 5, 4, 4, 7, 7, 33, 33, 33, 33, 33, 5, 5, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 33, 33, 33, 33, 5, 5] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603653035 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035 Building ZINC000603653035 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603653035 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 508) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(OCc2cccnc2)cc1) `ZINC000603653035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603653035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000603653035 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(OCc2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 5, 5, 4, 4, 8, 8, 41, 41, 41, 41, 41, 5, 5, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 41, 41, 41, 41, 5, 5] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 509) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(OCc2cccnc2)cc1) `ZINC000603653035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603653035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000603653035 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(OCc2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 5, 5, 4, 4, 7, 7, 33, 33, 33, 33, 33, 5, 5, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 33, 33, 33, 33, 5, 5] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603653035 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603653035 Building ZINC000603654160 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000603654160 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/510 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603654160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603654160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603654160 none O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 14, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 14, 12, 4, 15, 15, 15, 15, 25, 37, 37, 30, 37, 37, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 15, 15, 15, 15, 25, 25, 37, 37, 37, 37, 37, 15, 15, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/511 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/511' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603654160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603654160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603654160 none O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 14, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 14, 12, 4, 15, 15, 15, 15, 25, 37, 37, 30, 37, 37, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 15, 15, 15, 15, 25, 25, 37, 37, 37, 37, 37, 15, 15, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/512 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/512' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603654160.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000603654160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603654160 none O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 14, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 14, 11, 4, 15, 15, 15, 15, 25, 38, 38, 32, 38, 38, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 15, 15, 15, 15, 25, 25, 38, 38, 38, 38, 38, 15, 15, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/513 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/513' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603654160.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000603654160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603654160 none O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 14, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 14, 11, 4, 15, 15, 15, 15, 25, 38, 38, 32, 38, 38, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 15, 15, 15, 15, 25, 25, 38, 38, 38, 38, 38, 15, 15, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603654160 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 Building ZINC000603654160 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000603654160 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 510) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603654160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603654160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603654160 none O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 14, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 14, 12, 4, 15, 15, 15, 15, 25, 37, 37, 30, 37, 37, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 15, 15, 15, 15, 25, 25, 37, 37, 37, 37, 37, 15, 15, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 511) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603654160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603654160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603654160 none O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 14, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 14, 12, 4, 15, 15, 15, 15, 25, 37, 37, 30, 37, 37, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 15, 15, 15, 15, 25, 25, 37, 37, 37, 37, 37, 15, 15, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 512) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603654160.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000603654160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603654160 none O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 14, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 14, 11, 4, 15, 15, 15, 15, 25, 38, 38, 32, 38, 38, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 15, 15, 15, 15, 25, 25, 38, 38, 38, 38, 38, 15, 15, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 513) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603654160.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000603654160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603654160 none O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 14, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 14, 11, 4, 15, 15, 15, 15, 25, 38, 38, 32, 38, 38, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 15, 15, 15, 15, 25, 25, 38, 38, 38, 38, 38, 15, 15, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603654160 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 Building ZINC000603654160 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000603654160 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 510) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603654160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603654160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603654160 none O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 14, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 14, 12, 4, 15, 15, 15, 15, 25, 37, 37, 30, 37, 37, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 15, 15, 15, 15, 25, 25, 37, 37, 37, 37, 37, 15, 15, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 511) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603654160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603654160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603654160 none O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 14, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 14, 12, 4, 15, 15, 15, 15, 25, 37, 37, 30, 37, 37, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 15, 15, 15, 15, 25, 25, 37, 37, 37, 37, 37, 15, 15, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 512) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603654160.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000603654160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603654160 none O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 14, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 14, 11, 4, 15, 15, 15, 15, 25, 38, 38, 32, 38, 38, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 15, 15, 15, 15, 25, 25, 38, 38, 38, 38, 38, 15, 15, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 513) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603654160.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000603654160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603654160 none O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 14, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 14, 11, 4, 15, 15, 15, 15, 25, 38, 38, 32, 38, 38, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 15, 15, 15, 15, 25, 25, 38, 38, 38, 38, 38, 15, 15, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603654160 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 Building ZINC000603654160 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000603654160 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 510) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603654160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603654160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603654160 none O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 14, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 14, 12, 4, 15, 15, 15, 15, 25, 37, 37, 30, 37, 37, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 15, 15, 15, 15, 25, 25, 37, 37, 37, 37, 37, 15, 15, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 511) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603654160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603654160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603654160 none O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 14, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 14, 12, 4, 15, 15, 15, 15, 25, 37, 37, 30, 37, 37, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 15, 15, 15, 15, 25, 25, 37, 37, 37, 37, 37, 15, 15, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 512) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603654160.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000603654160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603654160 none O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 14, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 14, 11, 4, 15, 15, 15, 15, 25, 38, 38, 32, 38, 38, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 15, 15, 15, 15, 25, 25, 38, 38, 38, 38, 38, 15, 15, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 513) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603654160.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000603654160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603654160 none O=C(Nc1nc2c(s1)CCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 14, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 14, 11, 4, 15, 15, 15, 15, 25, 38, 38, 32, 38, 38, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 15, 15, 15, 15, 25, 25, 38, 38, 38, 38, 38, 15, 15, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603654160 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603654160 Building ZINC000603657198 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603657198 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/514 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCc1cc(c2ccc(F)cc2)no1)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603657198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603657198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603657198 none CN(CCCc1cc(c2ccc(F)cc2)no1)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 12, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 7, 10, 16, 36, 36, 36, 37, 37, 36, 36, 37, 37, 36, 36, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 11, 11, 16, 15, 36, 37, 37, 37, 37, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/515 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/515' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCc1cc(c2ccc(F)cc2)no1)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603657198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603657198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603657198 none CN(CCCc1cc(c2ccc(F)cc2)no1)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 12, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 7, 10, 16, 35, 35, 35, 36, 36, 35, 35, 36, 36, 35, 35, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 11, 11, 15, 16, 35, 36, 36, 36, 36, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603657198 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198 Building ZINC000603657198 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603657198 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 514) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCc1cc(c2ccc(F)cc2)no1)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603657198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603657198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603657198 none CN(CCCc1cc(c2ccc(F)cc2)no1)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 12, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 7, 10, 16, 36, 36, 36, 37, 37, 36, 36, 37, 37, 36, 36, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 11, 11, 16, 15, 36, 37, 37, 37, 37, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 515) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCc1cc(c2ccc(F)cc2)no1)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603657198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603657198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603657198 none CN(CCCc1cc(c2ccc(F)cc2)no1)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 12, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 7, 10, 16, 35, 35, 35, 36, 36, 35, 35, 36, 36, 35, 35, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 11, 11, 15, 16, 35, 36, 36, 36, 36, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603657198 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657198 Building ZINC000603657668 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603657668 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/516 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2nc(c3ccccc3)no2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603657668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603657668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603657668 none O=C(N1CCC(c2nc(c3ccccc3)no2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 5, 5, 5, 5, 32, 32, 32, 34, 34, 34, 34, 34, 32, 32, 5, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 34, 34, 34, 34, 34, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/517 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/517' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2nc(c3ccccc3)no2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603657668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603657668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603657668 none O=C(N1CCC(c2nc(c3ccccc3)no2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 6, 6, 6, 6, 33, 33, 33, 34, 34, 34, 34, 34, 33, 33, 6, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603657668 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668 Building ZINC000603657668 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603657668 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 516) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2nc(c3ccccc3)no2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603657668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603657668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603657668 none O=C(N1CCC(c2nc(c3ccccc3)no2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 5, 5, 5, 5, 32, 32, 32, 34, 34, 34, 34, 34, 32, 32, 5, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 34, 34, 34, 34, 34, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 517) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2nc(c3ccccc3)no2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603657668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603657668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603657668 none O=C(N1CCC(c2nc(c3ccccc3)no2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 6, 6, 6, 6, 33, 33, 33, 34, 34, 34, 34, 34, 33, 33, 6, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603657668 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603657668 Building ZINC000603681565 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603681565 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/518 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2[nH]c3ccc(Br)cc3c2C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603681565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603681565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000603681565 none O=C(N1CCc2[nH]c3ccc(Br)cc3c2C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 9, 9, 7, 9, 9, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/519 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/519' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2[nH]c3ccc(Br)cc3c2C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603681565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603681565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000603681565 none O=C(N1CCc2[nH]c3ccc(Br)cc3c2C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603681565 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565 Building ZINC000603681565 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603681565 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 518) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2[nH]c3ccc(Br)cc3c2C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603681565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603681565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000603681565 none O=C(N1CCc2[nH]c3ccc(Br)cc3c2C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 9, 9, 7, 9, 9, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 519) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2[nH]c3ccc(Br)cc3c2C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603681565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603681565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000603681565 none O=C(N1CCc2[nH]c3ccc(Br)cc3c2C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603681565 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603681565 Building ZINC000603684004 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603684004 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/520 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2[nH]c3c(cccc3Br)c2C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603684004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603684004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000603684004 none O=C(N1CCc2[nH]c3c(cccc3Br)c2C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 9, 9, 7, 9, 9, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/521 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/521' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2[nH]c3c(cccc3Br)c2C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603684004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603684004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000603684004 none O=C(N1CCc2[nH]c3c(cccc3Br)c2C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603684004 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004 Building ZINC000603684004 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603684004 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 520) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2[nH]c3c(cccc3Br)c2C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603684004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603684004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000603684004 none O=C(N1CCc2[nH]c3c(cccc3Br)c2C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 9, 9, 7, 9, 9, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 521) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2[nH]c3c(cccc3Br)c2C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000603684004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603684004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000603684004 none O=C(N1CCc2[nH]c3c(cccc3Br)c2C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603684004 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603684004 Building ZINC000603740307 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603740307 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/522 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cn1) `ZINC000603740307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603740307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603740307 none CCn1cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 10, 10, 7, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 10, 10, 11, 11, 11, 11, 11, 10, 7, 7, 3, 3, 3, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/523 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/523' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cn1) `ZINC000603740307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603740307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603740307 none CCn1cc(CN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 10, 10, 7, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 10, 10, 11, 11, 11, 11, 11, 10, 7, 7, 3, 3, 3, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603740307 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307 Building ZINC000603740307 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603740307 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 522) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cn1) `ZINC000603740307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603740307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603740307 none CCn1cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 10, 10, 7, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 10, 10, 11, 11, 11, 11, 11, 10, 7, 7, 3, 3, 3, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 523) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cn1) `ZINC000603740307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603740307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000603740307 none CCn1cc(CN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 10, 10, 7, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 10, 10, 11, 11, 11, 11, 11, 10, 7, 7, 3, 3, 3, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603740307 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603740307 Building ZINC000603930095 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603930095 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/524 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@@H](c1ccccc1)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000603930095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603930095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000603930095 none CCOC(=O)C[C@@H](c1ccccc1)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 19, 19, 9, 19, 5, 4, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 4, 4, 29, 29, 29, 29, 29, 9, 9, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 153 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/525 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@@H](c1ccccc1)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000603930095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603930095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000603930095 none CCOC(=O)C[C@@H](c1ccccc1)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 24, 24, 10, 24, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 5, 5, 32, 32, 32, 32, 32, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 5, 5, 5, 5] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 143 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603930095 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095 Building ZINC000603930095 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603930095 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 524) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/524: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@@H](c1ccccc1)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000603930095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603930095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000603930095 none CCOC(=O)C[C@@H](c1ccccc1)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 19, 19, 9, 19, 5, 4, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 4, 4, 29, 29, 29, 29, 29, 9, 9, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 153 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 525) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/525: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@@H](c1ccccc1)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000603930095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603930095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000603930095 none CCOC(=O)C[C@@H](c1ccccc1)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 24, 24, 10, 24, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 5, 5, 32, 32, 32, 32, 32, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 5, 5, 5, 5] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 143 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603930095 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930095 Building ZINC000603930096 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603930096 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/526 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@H](c1ccccc1)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000603930096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603930096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000603930096 none CCOC(=O)C[C@H](c1ccccc1)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 18, 18, 7, 18, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 4, 4, 28, 28, 28, 28, 28, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 158 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/527 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/527' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@H](c1ccccc1)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000603930096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603930096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000603930096 none CCOC(=O)C[C@H](c1ccccc1)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 20, 20, 10, 20, 6, 5, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 5, 5, 5, 29, 29, 29, 29, 29, 10, 10, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 5] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 149 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603930096 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096 Building ZINC000603930096 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000603930096 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 526) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/526: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@H](c1ccccc1)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000603930096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000603930096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000603930096 none CCOC(=O)C[C@H](c1ccccc1)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 18, 18, 7, 18, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 4, 4, 28, 28, 28, 28, 28, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 158 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 527) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/527: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@H](c1ccccc1)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000603930096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000603930096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000603930096 none CCOC(=O)C[C@H](c1ccccc1)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 20, 20, 10, 20, 6, 5, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 5, 5, 5, 29, 29, 29, 29, 29, 10, 10, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 5] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 149 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000603930096 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000603930096 Building ZINC000599647411 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000599647411 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/528 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)Nc3ccccc3F)cccc21) `ZINC000599647411.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000599647411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000599647411 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)Nc3ccccc3F)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 14, 15, 15, 17, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 14, 17, 46, 46, 46, 46, 5, 5, 5] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/529 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)Nc3ccccc3F)cccc21) `ZINC000599647411.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000599647411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000599647411 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)Nc3ccccc3F)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 13, 14, 14, 16, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 13, 16, 44, 44, 44, 44, 5, 5, 5] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000599647411 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411 Building ZINC000599647411 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000599647411 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 528) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)Nc3ccccc3F)cccc21) `ZINC000599647411.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000599647411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000599647411 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)Nc3ccccc3F)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 14, 15, 15, 17, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 14, 17, 46, 46, 46, 46, 5, 5, 5] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 529) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)Nc3ccccc3F)cccc21) `ZINC000599647411.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000599647411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000599647411 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)Nc3ccccc3F)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 13, 14, 14, 16, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 13, 16, 44, 44, 44, 44, 5, 5, 5] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000599647411 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000599647411 Building ZINC000604106519 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604106519 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/530 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(I)cc2Cl)cn1) `ZINC000604106519.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604106519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000604106519 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(I)cc2Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 18, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 20, 20, 11, 11, 1, 1, 1, 1, 5, 5, 5, 11, 11, 7, 11, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 5, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/531 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(I)cc2Cl)cn1) `ZINC000604106519.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604106519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000604106519 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(I)cc2Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 18, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 19, 19, 10, 10, 1, 1, 1, 1, 5, 5, 5, 11, 11, 5, 7, 11, 11, 11, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 5, 11, 11, 11, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604106519 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519 Building ZINC000604106519 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604106519 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 530) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(I)cc2Cl)cn1) `ZINC000604106519.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604106519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000604106519 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(I)cc2Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 18, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 20, 20, 11, 11, 1, 1, 1, 1, 5, 5, 5, 11, 11, 7, 11, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 5, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 531) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(I)cc2Cl)cn1) `ZINC000604106519.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604106519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000604106519 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(I)cc2Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 18, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 19, 19, 10, 10, 1, 1, 1, 1, 5, 5, 5, 11, 11, 5, 7, 11, 11, 11, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 5, 11, 11, 11, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604106519 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604106519 Building ZINC000604285267 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604285267 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/532 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCN(CC(C)C)C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1OC) `ZINC000604285267.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604285267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000604285267 none COc1ccc(CCN(CC(C)C)C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 10, 10, 10, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 20, 19, 19, 19, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 10, 20, 20, 20] 50 rigid atoms, others: [7, 8, 9, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/533 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCN(CC(C)C)C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1OC) `ZINC000604285267.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604285267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000604285267 none COc1ccc(CCN(CC(C)C)C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 10, 10, 10, 10, 4, 4, 2, 1, 2, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 27, 23, 23, 23, 10, 10, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 10, 27, 27, 27] 50 rigid atoms, others: [8, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604285267 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267 Building ZINC000604285267 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604285267 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 532) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCN(CC(C)C)C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1OC) `ZINC000604285267.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604285267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000604285267 none COc1ccc(CCN(CC(C)C)C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 10, 10, 10, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 20, 19, 19, 19, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 10, 20, 20, 20] 50 rigid atoms, others: [7, 8, 9, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 533) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCN(CC(C)C)C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1OC) `ZINC000604285267.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604285267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000604285267 none COc1ccc(CCN(CC(C)C)C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 10, 10, 10, 10, 4, 4, 2, 1, 2, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 27, 23, 23, 23, 10, 10, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 10, 27, 27, 27] 50 rigid atoms, others: [8, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604285267 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604285267 Building ZINC000604337625 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604337625 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/534 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nc(c2cccc(Cl)c2)no1) `ZINC000604337625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604337625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000604337625 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nc(c2cccc(Cl)c2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 30, 30, 30, 50, 50, 50, 50, 50, 50, 30, 30, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 3, 7, 7, 50, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/535 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nc(c2cccc(Cl)c2)no1) `ZINC000604337625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604337625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000604337625 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nc(c2cccc(Cl)c2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 33, 33, 33, 50, 50, 50, 50, 50, 50, 33, 33, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 2, 10, 10, 50, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604337625 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625 Building ZINC000604337625 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604337625 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 534) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nc(c2cccc(Cl)c2)no1) `ZINC000604337625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604337625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000604337625 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nc(c2cccc(Cl)c2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 30, 30, 30, 50, 50, 50, 50, 50, 50, 30, 30, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 3, 7, 7, 50, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 535) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/535: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nc(c2cccc(Cl)c2)no1) `ZINC000604337625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604337625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000604337625 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nc(c2cccc(Cl)c2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 33, 33, 33, 50, 50, 50, 50, 50, 50, 33, 33, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 2, 10, 10, 50, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604337625 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604337625 Building ZINC000604339367 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604339367 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/536 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nc(c2ccc(Cl)cc2)no1) `ZINC000604339367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604339367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000604339367 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nc(c2ccc(Cl)cc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 12, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 3, 12, 12, 48, 48, 48, 48] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/537 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nc(c2ccc(Cl)cc2)no1) `ZINC000604339367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604339367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000604339367 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nc(c2ccc(Cl)cc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 11, 11, 50, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604339367 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367 Building ZINC000604339367 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604339367 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 536) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nc(c2ccc(Cl)cc2)no1) `ZINC000604339367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604339367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000604339367 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nc(c2ccc(Cl)cc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 12, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 3, 12, 12, 48, 48, 48, 48] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 537) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nc(c2ccc(Cl)cc2)no1) `ZINC000604339367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604339367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000604339367 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nc(c2ccc(Cl)cc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 11, 11, 50, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604339367 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604339367 Building ZINC000604568107 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604568107 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/538 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1occc1CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](C)c1ccccn1) `ZINC000604568107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604568107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000604568107 none COC(=O)c1occc1CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](C)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 12, 22, 12, 12, 12, 12, 8, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 10, 10, 10, 10, 10, 22, 22, 22, 12, 12, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 10, 10, 10, 10] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/539 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/539' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1occc1CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](C)c1ccccn1) `ZINC000604568107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604568107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000604568107 none COC(=O)c1occc1CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](C)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 11, 23, 11, 11, 11, 11, 9, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 6, 6, 6, 11, 11, 11, 11, 11, 23, 23, 23, 11, 11, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 11, 11, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604568107 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107 Building ZINC000604568107 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604568107 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 538) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1occc1CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](C)c1ccccn1) `ZINC000604568107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604568107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000604568107 none COC(=O)c1occc1CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](C)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 12, 22, 12, 12, 12, 12, 8, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 10, 10, 10, 10, 10, 22, 22, 22, 12, 12, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 10, 10, 10, 10] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 539) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1occc1CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](C)c1ccccn1) `ZINC000604568107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604568107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000604568107 none COC(=O)c1occc1CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](C)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 11, 23, 11, 11, 11, 11, 9, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 6, 6, 6, 11, 11, 11, 11, 11, 23, 23, 23, 11, 11, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 11, 11, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604568107 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568107 Building ZINC000604568110 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604568110 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/540 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1occc1CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](C)c1ccccn1) `ZINC000604568110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604568110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000604568110 none COC(=O)c1occc1CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](C)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 11, 23, 11, 11, 11, 11, 9, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 6, 6, 6, 11, 11, 11, 11, 11, 23, 23, 23, 11, 11, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 11, 11, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/541 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/541' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1occc1CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](C)c1ccccn1) `ZINC000604568110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604568110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000604568110 none COC(=O)c1occc1CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](C)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 12, 22, 12, 12, 12, 12, 8, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 10, 10, 10, 10, 10, 22, 22, 22, 12, 12, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 10, 10, 10, 10] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604568110 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110 Building ZINC000604568110 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604568110 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 540) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1occc1CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](C)c1ccccn1) `ZINC000604568110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604568110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000604568110 none COC(=O)c1occc1CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](C)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 11, 23, 11, 11, 11, 11, 9, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 6, 6, 6, 11, 11, 11, 11, 11, 23, 23, 23, 11, 11, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 11, 11, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 541) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1occc1CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](C)c1ccccn1) `ZINC000604568110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604568110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000604568110 none COC(=O)c1occc1CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](C)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 12, 22, 12, 12, 12, 12, 8, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 10, 10, 10, 10, 10, 22, 22, 22, 12, 12, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 10, 10, 10, 10] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604568110 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604568110 Building ZINC000604735139 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604735139 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/542 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCc1ccc(Br)cc1F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000604735139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604735139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000604735139 none O=C(NCCCc1ccc(Br)cc1F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 15, 20, 27, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 27, 27, 27, 27, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/543 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/543' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCc1ccc(Br)cc1F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000604735139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604735139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000604735139 none O=C(NCCCc1ccc(Br)cc1F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 15, 20, 27, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 27, 27, 27, 27, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604735139 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139 Building ZINC000604735139 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604735139 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 542) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCc1ccc(Br)cc1F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000604735139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604735139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000604735139 none O=C(NCCCc1ccc(Br)cc1F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 15, 20, 27, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 27, 27, 27, 27, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 543) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCc1ccc(Br)cc1F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000604735139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604735139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000604735139 none O=C(NCCCc1ccc(Br)cc1F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 15, 20, 27, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 27, 27, 27, 27, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604735139 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604735139 Building ZINC000604845553 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604845553 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/544 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)c(NC(=O)c2ccncc2)c(Cl)c1) `ZINC000604845553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604845553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000604845553 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)c(NC(=O)c2ccncc2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 5, 5, 33, 34, 33, 44, 46, 41, 47, 44, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 14, 34, 44, 47, 47, 44, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/545 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/545' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)c(NC(=O)c2ccncc2)c(Cl)c1) `ZINC000604845553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604845553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000604845553 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)c(NC(=O)c2ccncc2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 22, 22, 22, 16, 22, 41, 41, 41, 47, 47, 47, 47, 47, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 22, 41, 47, 47, 47, 47, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604845553 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553 Building ZINC000604845553 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604845553 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 544) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)c(NC(=O)c2ccncc2)c(Cl)c1) `ZINC000604845553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604845553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000604845553 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)c(NC(=O)c2ccncc2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 5, 5, 33, 34, 33, 44, 46, 41, 47, 44, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 14, 34, 44, 47, 47, 44, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 545) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)c(NC(=O)c2ccncc2)c(Cl)c1) `ZINC000604845553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604845553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000604845553 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)c(NC(=O)c2ccncc2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 22, 22, 22, 16, 22, 41, 41, 41, 47, 47, 47, 47, 47, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 22, 41, 47, 47, 47, 47, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604845553 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604845553 Building ZINC000604859125 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604859125 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/546 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1ccco1) `ZINC000604859125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604859125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000604859125 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 2, 2, 2, 16, 16, 7, 16, 2, 2, 2, 4, 4, 4, 4, 4, 4, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 62 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/547 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1ccco1) `ZINC000604859125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604859125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000604859125 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 2, 2, 2, 16, 16, 2, 16, 2, 2, 2, 5, 5, 5, 5, 5, 5, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 58 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604859125 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125 Building ZINC000604859125 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604859125 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 546) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/546: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1ccco1) `ZINC000604859125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604859125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000604859125 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 2, 2, 2, 16, 16, 7, 16, 2, 2, 2, 4, 4, 4, 4, 4, 4, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 62 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 547) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/547: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1ccco1) `ZINC000604859125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604859125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000604859125 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 2, 2, 2, 16, 16, 2, 16, 2, 2, 2, 5, 5, 5, 5, 5, 5, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 58 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604859125 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859125 Building ZINC000604859126 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604859126 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/548 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1ccco1) `ZINC000604859126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604859126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000604859126 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 2, 5, 5, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 6, 6, 6, 6, 6, 6, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 67 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/549 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1ccco1) `ZINC000604859126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604859126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000604859126 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 2, 2, 2, 18, 18, 18, 18, 2, 2, 2, 4, 4, 4, 4, 4, 4, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 40 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604859126 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126 Building ZINC000604859126 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604859126 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 548) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/548: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1ccco1) `ZINC000604859126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604859126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000604859126 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 2, 5, 5, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 6, 6, 6, 6, 6, 6, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 67 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 549) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1ccco1) `ZINC000604859126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604859126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000604859126 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 2, 2, 2, 18, 18, 18, 18, 2, 2, 2, 4, 4, 4, 4, 4, 4, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 40 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604859126 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604859126 Building ZINC000604946070 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604946070 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/550 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1ccc(Br)cc1) `ZINC000604946070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604946070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000604946070 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 1, 1, 1, 1, 3, 3, 3, 17, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 3, 17, 17, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 156 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/551 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/551' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1ccc(Br)cc1) `ZINC000604946070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604946070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000604946070 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 7, 9, 9, 4, 4, 1, 1, 1, 1, 4, 4, 4, 19, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 9, 9, 7, 9, 9, 4, 4, 4, 4, 19, 19, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604946070 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070 Building ZINC000604946070 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604946070 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 550) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1ccc(Br)cc1) `ZINC000604946070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604946070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000604946070 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 1, 1, 1, 1, 3, 3, 3, 17, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 3, 17, 17, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 156 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 551) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1ccc(Br)cc1) `ZINC000604946070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604946070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000604946070 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 7, 9, 9, 4, 4, 1, 1, 1, 1, 4, 4, 4, 19, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 9, 9, 7, 9, 9, 4, 4, 4, 4, 19, 19, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604946070 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604946070 Building ZINC000604958911 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000604958911 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/552 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604958911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958911 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 5, 5, 9, 26, 26, 26, 26, 26, 26, 37, 37, 26, 26, 37, 37, 37, 26, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 4, 5, 26, 26, 26, 26, 26, 26, 37, 37, 37, 37, 37, 37, 26, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 145 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/553 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/553' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604958911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958911 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 5, 5, 9, 26, 26, 26, 26, 26, 26, 37, 37, 26, 26, 37, 37, 37, 26, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 4, 5, 26, 26, 26, 26, 26, 26, 37, 37, 37, 37, 37, 37, 26, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 145 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/554 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/554' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958911.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000604958911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958911 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 9, 23, 23, 23, 23, 23, 23, 39, 39, 23, 23, 39, 39, 39, 23, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 4, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/555 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/555' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958911.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000604958911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958911 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 9, 23, 23, 23, 23, 23, 23, 39, 39, 23, 23, 39, 39, 39, 23, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 4, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604958911 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 Building ZINC000604958911 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000604958911 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 552) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/552: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604958911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958911 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 5, 5, 9, 26, 26, 26, 26, 26, 26, 37, 37, 26, 26, 37, 37, 37, 26, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 4, 5, 26, 26, 26, 26, 26, 26, 37, 37, 37, 37, 37, 37, 26, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 145 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 553) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/553: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604958911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958911 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 5, 5, 9, 26, 26, 26, 26, 26, 26, 37, 37, 26, 26, 37, 37, 37, 26, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 4, 5, 26, 26, 26, 26, 26, 26, 37, 37, 37, 37, 37, 37, 26, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 145 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 554) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958911.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000604958911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958911 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 9, 23, 23, 23, 23, 23, 23, 39, 39, 23, 23, 39, 39, 39, 23, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 4, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 555) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958911.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000604958911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958911 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 9, 23, 23, 23, 23, 23, 23, 39, 39, 23, 23, 39, 39, 39, 23, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 4, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604958911 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 Building ZINC000604958911 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000604958911 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 552) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/552: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604958911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958911 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 5, 5, 9, 26, 26, 26, 26, 26, 26, 37, 37, 26, 26, 37, 37, 37, 26, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 4, 5, 26, 26, 26, 26, 26, 26, 37, 37, 37, 37, 37, 37, 26, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 145 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 553) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/553: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604958911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958911 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 5, 5, 9, 26, 26, 26, 26, 26, 26, 37, 37, 26, 26, 37, 37, 37, 26, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 4, 5, 26, 26, 26, 26, 26, 26, 37, 37, 37, 37, 37, 37, 26, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 145 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 554) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958911.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000604958911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958911 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 9, 23, 23, 23, 23, 23, 23, 39, 39, 23, 23, 39, 39, 39, 23, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 4, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 555) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958911.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000604958911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958911 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 9, 23, 23, 23, 23, 23, 23, 39, 39, 23, 23, 39, 39, 39, 23, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 4, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604958911 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 Building ZINC000604958911 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000604958911 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 552) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/552: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604958911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958911 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 5, 5, 9, 26, 26, 26, 26, 26, 26, 37, 37, 26, 26, 37, 37, 37, 26, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 4, 5, 26, 26, 26, 26, 26, 26, 37, 37, 37, 37, 37, 37, 26, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 145 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 553) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/553: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604958911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958911 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 5, 5, 9, 26, 26, 26, 26, 26, 26, 37, 37, 26, 26, 37, 37, 37, 26, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 4, 5, 26, 26, 26, 26, 26, 26, 37, 37, 37, 37, 37, 37, 26, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 145 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 554) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958911.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000604958911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958911 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 9, 23, 23, 23, 23, 23, 23, 39, 39, 23, 23, 39, 39, 39, 23, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 4, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 555) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958911.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000604958911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958911 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 9, 23, 23, 23, 23, 23, 23, 39, 39, 23, 23, 39, 39, 39, 23, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 4, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604958911 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958911 Building ZINC000604958912 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000604958912 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/556 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604958912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958912 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 5, 5, 10, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 39, 23, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 5, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 107 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/557 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/557' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604958912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958912 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 5, 5, 10, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 39, 23, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 5, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 107 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/558 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/558' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958912.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000604958912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958912 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 8, 10, 10, 4, 4, 1, 1, 1, 1, 5, 5, 9, 25, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 36, 36, 25, 4, 4, 4, 10, 10, 10, 10, 10, 4, 4, 4, 5, 25, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 36, 25, 25] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/559 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/559' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958912.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000604958912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958912 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 8, 10, 10, 4, 4, 1, 1, 1, 1, 5, 5, 9, 25, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 36, 36, 25, 4, 4, 4, 10, 10, 10, 10, 10, 4, 4, 4, 5, 25, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 36, 25, 25] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604958912 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 Building ZINC000604958912 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000604958912 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 556) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604958912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958912 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 5, 5, 10, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 39, 23, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 5, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 107 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 557) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604958912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958912 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 5, 5, 10, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 39, 23, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 5, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 107 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 558) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958912.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000604958912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958912 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 8, 10, 10, 4, 4, 1, 1, 1, 1, 5, 5, 9, 25, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 36, 36, 25, 4, 4, 4, 10, 10, 10, 10, 10, 4, 4, 4, 5, 25, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 36, 25, 25] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 559) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958912.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000604958912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958912 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 8, 10, 10, 4, 4, 1, 1, 1, 1, 5, 5, 9, 25, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 36, 36, 25, 4, 4, 4, 10, 10, 10, 10, 10, 4, 4, 4, 5, 25, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 36, 25, 25] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604958912 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 Building ZINC000604958912 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000604958912 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 556) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604958912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958912 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 5, 5, 10, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 39, 23, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 5, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 107 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 557) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604958912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958912 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 5, 5, 10, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 39, 23, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 5, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 107 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 558) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958912.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000604958912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958912 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 8, 10, 10, 4, 4, 1, 1, 1, 1, 5, 5, 9, 25, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 36, 36, 25, 4, 4, 4, 10, 10, 10, 10, 10, 4, 4, 4, 5, 25, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 36, 25, 25] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 559) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958912.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000604958912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958912 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 8, 10, 10, 4, 4, 1, 1, 1, 1, 5, 5, 9, 25, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 36, 36, 25, 4, 4, 4, 10, 10, 10, 10, 10, 4, 4, 4, 5, 25, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 36, 25, 25] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604958912 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 Building ZINC000604958912 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000604958912 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 556) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604958912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958912 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 5, 5, 10, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 39, 23, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 5, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 107 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 557) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604958912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958912 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 5, 5, 10, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 39, 23, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 5, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 107 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 558) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958912.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000604958912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958912 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 8, 10, 10, 4, 4, 1, 1, 1, 1, 5, 5, 9, 25, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 36, 36, 25, 4, 4, 4, 10, 10, 10, 10, 10, 4, 4, 4, 5, 25, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 36, 25, 25] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 559) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1) `ZINC000604958912.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000604958912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000604958912 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(F)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 8, 10, 10, 4, 4, 1, 1, 1, 1, 5, 5, 9, 25, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 36, 36, 25, 4, 4, 4, 10, 10, 10, 10, 10, 4, 4, 4, 5, 25, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 36, 25, 25] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000604958912 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000604958912 Building ZINC000605023962 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605023962 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/560 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CC(C)(C)C) `ZINC000605023962.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605023962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000605023962 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 12, 12, 36, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 107 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/561 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/561' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CC(C)(C)C) `ZINC000605023962.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605023962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000605023962 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 13, 13, 42, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 112 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605023962 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962 Building ZINC000605023962 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605023962 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 560) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CC(C)(C)C) `ZINC000605023962.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605023962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000605023962 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 12, 12, 36, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 107 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 561) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CC(C)(C)C) `ZINC000605023962.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605023962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000605023962 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 13, 13, 42, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 112 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605023962 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023962 Building ZINC000605023963 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605023963 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/562 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CC(C)(C)C) `ZINC000605023963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605023963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000605023963 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 13, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 11, 11, 3, 11, 3, 3, 3, 2, 13, 13, 42, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 120 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/563 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/563' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)CC(C)(C)C) `ZINC000605023963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605023963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000605023963 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)CC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 11, 11, 3, 11, 3, 3, 3, 2, 12, 12, 36, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 105 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605023963 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963 Building ZINC000605023963 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605023963 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 562) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CC(C)(C)C) `ZINC000605023963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605023963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000605023963 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 13, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 11, 11, 3, 11, 3, 3, 3, 2, 13, 13, 42, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 120 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 563) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)CC(C)(C)C) `ZINC000605023963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605023963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000605023963 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)CC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 11, 11, 3, 11, 3, 3, 3, 2, 12, 12, 36, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 105 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605023963 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605023963 Building ZINC000605274870 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605274870 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/564 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccnc(Oc2ccccc2Br)c1) `ZINC000605274870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605274870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000605274870 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccnc(Oc2ccccc2Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 33, 49, 49, 47, 49, 49, 49, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 49, 49, 48, 49, 7] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/565 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/565' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccnc(Oc2ccccc2Br)c1) `ZINC000605274870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605274870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000605274870 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccnc(Oc2ccccc2Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 31, 47, 47, 31, 47, 47, 47, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 47, 47, 45, 47, 7] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605274870 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870 Building ZINC000605274870 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605274870 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 564) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccnc(Oc2ccccc2Br)c1) `ZINC000605274870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605274870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000605274870 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccnc(Oc2ccccc2Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 33, 49, 49, 47, 49, 49, 49, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 49, 49, 48, 49, 7] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 565) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccnc(Oc2ccccc2Br)c1) `ZINC000605274870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605274870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000605274870 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccnc(Oc2ccccc2Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 31, 47, 47, 31, 47, 47, 47, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 47, 47, 45, 47, 7] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605274870 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605274870 Building ZINC000605367497 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605367497 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/566 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(Br)cc1) `ZINC000605367497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605367497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000605367497 none CCCCOCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 13, 13, 11, 10, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 5, 6, 6, 5, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 13, 13, 11, 11, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 144 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/567 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/567' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(Br)cc1) `ZINC000605367497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605367497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000605367497 none CCCCOCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 14, 14, 12, 10, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 32, 14, 14, 12, 12, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 144 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605367497 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497 Building ZINC000605367497 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605367497 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 566) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(Br)cc1) `ZINC000605367497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605367497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000605367497 none CCCCOCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 13, 13, 11, 10, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 5, 6, 6, 5, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 13, 13, 11, 11, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 144 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 567) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(Br)cc1) `ZINC000605367497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605367497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000605367497 none CCCCOCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 14, 14, 12, 10, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 32, 14, 14, 12, 12, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 144 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605367497 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605367497 Building ZINC000605438695 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605438695 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/568 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CN1CCCC1)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000605438695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605438695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000605438695 none CC[C@@H](CN1CCCC1)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 10, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 4, 4, 4, 4, 4, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 1, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3] 50 rigid atoms, others: [2, 10, 11, 12, 13, 14, 47, 15] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 88 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/569 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/569' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CN1CCCC1)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000605438695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605438695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000605438695 none CC[C@@H](CN1CCCC1)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 10, 10, 10, 10, 10, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 5, 5, 5, 5, 5, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605438695 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695 Building ZINC000605438695 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605438695 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 568) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CN1CCCC1)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000605438695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605438695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000605438695 none CC[C@@H](CN1CCCC1)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 10, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 4, 4, 4, 4, 4, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 1, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3] 50 rigid atoms, others: [2, 10, 11, 12, 13, 14, 47, 15] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 88 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 569) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CN1CCCC1)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000605438695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605438695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000605438695 none CC[C@@H](CN1CCCC1)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 10, 10, 10, 10, 10, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 5, 5, 5, 5, 5, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605438695 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438695 Building ZINC000605438705 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605438705 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/570 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CN1CCCC1)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000605438705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605438705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000605438705 none CC[C@H](CN1CCCC1)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 5, 2, 5, 5, 11, 11, 11, 11, 11, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 6, 6, 6, 6, 6, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/571 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/571' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CN1CCCC1)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000605438705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605438705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000605438705 none CC[C@H](CN1CCCC1)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 9, 14, 14, 14, 14, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 4, 15, 15, 15, 15, 15, 15, 4, 4, 5, 5, 5, 5, 5, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 2, 4, 4, 4, 15, 15, 8, 15, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 102 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605438705 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705 Building ZINC000605438705 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605438705 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 570) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CN1CCCC1)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000605438705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605438705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000605438705 none CC[C@H](CN1CCCC1)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 5, 2, 5, 5, 11, 11, 11, 11, 11, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 6, 6, 6, 6, 6, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 571) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CN1CCCC1)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000605438705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605438705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000605438705 none CC[C@H](CN1CCCC1)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 9, 14, 14, 14, 14, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 4, 15, 15, 15, 15, 15, 15, 4, 4, 5, 5, 5, 5, 5, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 2, 4, 4, 4, 15, 15, 8, 15, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 102 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605438705 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605438705 Building ZINC000605441125 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605441125 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/572 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(CC(F)F)c1) `ZINC000605441125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605441125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000605441125 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(CC(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 11, 12, 12, 6, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 2, 6, 11, 11, 12, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/573 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/573' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(CC(F)F)c1) `ZINC000605441125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605441125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000605441125 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(CC(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 10, 11, 11, 5, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 5, 10, 10, 11, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605441125 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125 Building ZINC000605441125 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605441125 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 572) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(CC(F)F)c1) `ZINC000605441125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605441125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000605441125 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(CC(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 11, 12, 12, 6, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 2, 6, 11, 11, 12, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 573) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(CC(F)F)c1) `ZINC000605441125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605441125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000605441125 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(CC(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 10, 11, 11, 5, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 5, 10, 10, 11, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605441125 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605441125 Building ZINC000605446829 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000605446829 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/574 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](CCOc3ccc(Br)cc3)CC2)cc1) `ZINC000605446829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605446829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000605446829 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](CCOc3ccc(Br)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 21, 25, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 21, 21, 25, 25, 50, 50, 50, 50, 11, 11, 11, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/575 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/575' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](CCOc3ccc(Br)cc3)CC2)cc1) `ZINC000605446829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605446829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000605446829 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](CCOc3ccc(Br)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 21, 25, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 21, 21, 25, 25, 50, 50, 50, 50, 11, 11, 11, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/576 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/576' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](CCOc3ccc(Br)cc3)CC2)cc1) `ZINC000605446829.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000605446829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000605446829 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](CCOc3ccc(Br)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 22, 26, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 22, 22, 26, 26, 50, 50, 50, 50, 11, 11, 11, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/577 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/577' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](CCOc3ccc(Br)cc3)CC2)cc1) `ZINC000605446829.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000605446829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000605446829 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](CCOc3ccc(Br)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 21, 25, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 21, 21, 25, 25, 50, 50, 50, 50, 11, 11, 11, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605446829 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 Building ZINC000605446829 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000605446829 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 574) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](CCOc3ccc(Br)cc3)CC2)cc1) `ZINC000605446829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605446829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000605446829 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](CCOc3ccc(Br)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 21, 25, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 21, 21, 25, 25, 50, 50, 50, 50, 11, 11, 11, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 575) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](CCOc3ccc(Br)cc3)CC2)cc1) `ZINC000605446829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605446829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000605446829 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](CCOc3ccc(Br)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 21, 25, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 21, 21, 25, 25, 50, 50, 50, 50, 11, 11, 11, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 576) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](CCOc3ccc(Br)cc3)CC2)cc1) `ZINC000605446829.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000605446829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000605446829 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](CCOc3ccc(Br)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 22, 26, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 22, 22, 26, 26, 50, 50, 50, 50, 11, 11, 11, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 577) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/577: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](CCOc3ccc(Br)cc3)CC2)cc1) `ZINC000605446829.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000605446829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000605446829 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](CCOc3ccc(Br)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 21, 25, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 21, 21, 25, 25, 50, 50, 50, 50, 11, 11, 11, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605446829 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 Building ZINC000605446829 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000605446829 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 574) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](CCOc3ccc(Br)cc3)CC2)cc1) `ZINC000605446829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605446829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000605446829 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](CCOc3ccc(Br)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 21, 25, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 21, 21, 25, 25, 50, 50, 50, 50, 11, 11, 11, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 575) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](CCOc3ccc(Br)cc3)CC2)cc1) `ZINC000605446829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605446829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000605446829 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](CCOc3ccc(Br)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 21, 25, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 21, 21, 25, 25, 50, 50, 50, 50, 11, 11, 11, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 576) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](CCOc3ccc(Br)cc3)CC2)cc1) `ZINC000605446829.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000605446829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000605446829 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](CCOc3ccc(Br)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 22, 26, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 22, 22, 26, 26, 50, 50, 50, 50, 11, 11, 11, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 577) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/577: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](CCOc3ccc(Br)cc3)CC2)cc1) `ZINC000605446829.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000605446829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000605446829 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](CCOc3ccc(Br)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 21, 25, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 21, 21, 25, 25, 50, 50, 50, 50, 11, 11, 11, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605446829 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 Building ZINC000605446829 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000605446829 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 574) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](CCOc3ccc(Br)cc3)CC2)cc1) `ZINC000605446829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605446829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000605446829 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](CCOc3ccc(Br)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 21, 25, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 21, 21, 25, 25, 50, 50, 50, 50, 11, 11, 11, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 575) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](CCOc3ccc(Br)cc3)CC2)cc1) `ZINC000605446829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605446829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000605446829 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](CCOc3ccc(Br)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 21, 25, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 21, 21, 25, 25, 50, 50, 50, 50, 11, 11, 11, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 576) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](CCOc3ccc(Br)cc3)CC2)cc1) `ZINC000605446829.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000605446829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000605446829 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](CCOc3ccc(Br)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 22, 26, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 22, 22, 26, 26, 50, 50, 50, 50, 11, 11, 11, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 577) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/577: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](CCOc3ccc(Br)cc3)CC2)cc1) `ZINC000605446829.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000605446829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000605446829 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](CCOc3ccc(Br)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 21, 25, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 21, 21, 25, 25, 50, 50, 50, 50, 11, 11, 11, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605446829 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605446829 Building ZINC000605474172 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605474172 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/578 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1)C1CC1) `ZINC000605474172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605474172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000605474172 none CC(=O)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 18, 7, 3, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 9, 9, 35, 35, 35, 35, 35, 35, 18, 18, 9, 9, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 9, 9, 35, 35, 35, 35, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/579 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/579' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1)C1CC1) `ZINC000605474172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605474172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000605474172 none CC(=O)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 16, 2, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 9, 9, 37, 37, 37, 37, 37, 37, 16, 16, 9, 9, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 9, 9, 37, 37, 37, 37, 37] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605474172 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172 Building ZINC000605474172 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605474172 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 578) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/578: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1)C1CC1) `ZINC000605474172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605474172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000605474172 none CC(=O)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 18, 7, 3, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 9, 9, 35, 35, 35, 35, 35, 35, 18, 18, 9, 9, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 9, 9, 35, 35, 35, 35, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 579) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/579: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1)C1CC1) `ZINC000605474172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605474172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000605474172 none CC(=O)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 16, 2, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 9, 9, 37, 37, 37, 37, 37, 37, 16, 16, 9, 9, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 9, 9, 37, 37, 37, 37, 37] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605474172 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605474172 Building ZINC000605635404 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605635404 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/580 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)c1cc2ccccc2o1) `ZINC000605635404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605635404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000605635404 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)c1cc2ccccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 20, 32, 32, 46, 46, 47, 47, 47, 47, 47, 47, 47, 47, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 7, 7, 7, 7, 20, 20, 32, 32, 32, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 155 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/581 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/581' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)c1cc2ccccc2o1) `ZINC000605635404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605635404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000605635404 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)c1cc2ccccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 5, 5, 5, 16, 29, 29, 44, 44, 46, 46, 46, 46, 46, 46, 46, 46, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 2, 5, 16, 16, 29, 29, 29, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 158 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605635404 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404 Building ZINC000605635404 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605635404 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 580) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/580: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)c1cc2ccccc2o1) `ZINC000605635404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605635404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000605635404 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)c1cc2ccccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 20, 32, 32, 46, 46, 47, 47, 47, 47, 47, 47, 47, 47, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 7, 7, 7, 7, 20, 20, 32, 32, 32, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 155 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 581) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)c1cc2ccccc2o1) `ZINC000605635404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605635404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000605635404 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)c1cc2ccccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 5, 5, 5, 16, 29, 29, 44, 44, 46, 46, 46, 46, 46, 46, 46, 46, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 2, 5, 16, 16, 29, 29, 29, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 158 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605635404 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605635404 Building ZINC000605888621 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605888621 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/582 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(NC2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)c1) `ZINC000605888621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605888621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000605888621 none COc1cccc(NC2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 40, 40, 40, 40, 40, 10, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 3, 3, 40, 48, 48, 48, 40, 40, 40, 10, 3, 3, 3, 3, 3, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 3, 3, 3, 3, 40] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 84 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/583 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/583' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(NC2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)c1) `ZINC000605888621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605888621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000605888621 none COc1cccc(NC2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 40, 40, 40, 40, 40, 11, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 3, 3, 40, 48, 48, 48, 40, 40, 40, 11, 3, 3, 3, 3, 3, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 3, 3, 3, 3, 40] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 90 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605888621 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621 Building ZINC000605888621 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605888621 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 582) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(NC2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)c1) `ZINC000605888621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605888621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000605888621 none COc1cccc(NC2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 40, 40, 40, 40, 40, 10, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 3, 3, 40, 48, 48, 48, 40, 40, 40, 10, 3, 3, 3, 3, 3, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 3, 3, 3, 3, 40] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 84 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 583) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(NC2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)c1) `ZINC000605888621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605888621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000605888621 none COc1cccc(NC2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 40, 40, 40, 40, 40, 11, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 3, 3, 40, 48, 48, 48, 40, 40, 40, 11, 3, 3, 3, 3, 3, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 3, 3, 3, 3, 40] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 90 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000605888621 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000605888621 Building ZINC000606222622 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000606222622 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/584 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc([C@@H]2Cc3ccccc3CN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)o1) `ZINC000606222622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000606222622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000606222622 none Cc1nnc([C@@H]2Cc3ccccc3CN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/585 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/585' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc([C@@H]2Cc3ccccc3CN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)o1) `ZINC000606222622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000606222622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000606222622 none Cc1nnc([C@@H]2Cc3ccccc3CN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 27, 27, 27, 27, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000606222622 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622 Building ZINC000606222622 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000606222622 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 584) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc([C@@H]2Cc3ccccc3CN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)o1) `ZINC000606222622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000606222622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000606222622 none Cc1nnc([C@@H]2Cc3ccccc3CN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 585) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc([C@@H]2Cc3ccccc3CN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)o1) `ZINC000606222622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000606222622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000606222622 none Cc1nnc([C@@H]2Cc3ccccc3CN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 27, 27, 27, 27, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000606222622 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222622 Building ZINC000606222623 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000606222623 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/586 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc([C@H]2Cc3ccccc3CN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)o1) `ZINC000606222623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000606222623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000606222623 none Cc1nnc([C@H]2Cc3ccccc3CN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 5, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 28, 28, 28, 28, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 66 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/587 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/587' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc([C@H]2Cc3ccccc3CN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)o1) `ZINC000606222623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000606222623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000606222623 none Cc1nnc([C@H]2Cc3ccccc3CN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000606222623 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623 Building ZINC000606222623 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000606222623 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 586) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/586: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc([C@H]2Cc3ccccc3CN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)o1) `ZINC000606222623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000606222623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000606222623 none Cc1nnc([C@H]2Cc3ccccc3CN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 5, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 28, 28, 28, 28, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 66 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 587) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/587: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc([C@H]2Cc3ccccc3CN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)o1) `ZINC000606222623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000606222623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000606222623 none Cc1nnc([C@H]2Cc3ccccc3CN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000606222623 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606222623 Building ZINC000606537383 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000606537383 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/588 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(O)c(F)c1) `ZINC000606537383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000606537383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000606537383 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(O)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 15, 15, 30, 15] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/589 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/589' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(O)c(F)c1) `ZINC000606537383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000606537383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000606537383 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(O)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 14, 14, 28, 14] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000606537383 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383 Building ZINC000606537383 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000606537383 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 588) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/588: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(O)c(F)c1) `ZINC000606537383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000606537383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000606537383 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(O)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 15, 15, 30, 15] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 589) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/589: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(O)c(F)c1) `ZINC000606537383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000606537383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000606537383 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(O)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 14, 14, 28, 14] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000606537383 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606537383 Building ZINC000533956638 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000533956638 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/590 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2Cl)c2ccc(OC)cc2OC)cn1) `ZINC000533956638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000533956638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000533956638 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2Cl)c2ccc(OC)cc2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 8, 8, 6, 8, 8, 8, 6, 9, 9, 6, 9, 16, 9, 9, 9, 11, 6, 6, 15, 15, 15, 15, 15, 6, 4, 8, 8, 6, 8, 9, 9, 16, 16, 16, 9, 11, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/591 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/591' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2Cl)c2ccc(OC)cc2OC)cn1) `ZINC000533956638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000533956638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000533956638 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2Cl)c2ccc(OC)cc2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 7, 7, 6, 7, 7, 7, 6, 9, 9, 6, 9, 17, 9, 9, 9, 12, 6, 6, 16, 16, 16, 16, 16, 6, 4, 7, 7, 6, 7, 9, 9, 17, 17, 17, 9, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000533956638 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638 Building ZINC000533956638 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000533956638 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 590) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/590: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2Cl)c2ccc(OC)cc2OC)cn1) `ZINC000533956638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000533956638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000533956638 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2Cl)c2ccc(OC)cc2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 8, 8, 6, 8, 8, 8, 6, 9, 9, 6, 9, 16, 9, 9, 9, 11, 6, 6, 15, 15, 15, 15, 15, 6, 4, 8, 8, 6, 8, 9, 9, 16, 16, 16, 9, 11, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 591) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/591: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2Cl)c2ccc(OC)cc2OC)cn1) `ZINC000533956638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000533956638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000533956638 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2Cl)c2ccc(OC)cc2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 7, 7, 6, 7, 7, 7, 6, 9, 9, 6, 9, 17, 9, 9, 9, 12, 6, 6, 16, 16, 16, 16, 16, 6, 4, 7, 7, 6, 7, 9, 9, 17, 17, 17, 9, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000533956638 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956638 Building ZINC000533956639 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000533956639 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/592 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2Cl)c2ccc(OC)cc2OC)cn1) `ZINC000533956639.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000533956639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000533956639 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2Cl)c2ccc(OC)cc2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 7, 7, 6, 7, 7, 7, 6, 9, 9, 6, 9, 17, 9, 9, 9, 12, 6, 6, 16, 16, 16, 16, 16, 6, 4, 7, 7, 6, 7, 9, 9, 17, 17, 17, 9, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/593 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/593' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2Cl)c2ccc(OC)cc2OC)cn1) `ZINC000533956639.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000533956639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000533956639 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2Cl)c2ccc(OC)cc2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 7, 7, 6, 7, 7, 7, 6, 9, 9, 6, 9, 16, 9, 9, 9, 11, 6, 6, 15, 15, 15, 15, 15, 6, 4, 7, 7, 6, 7, 9, 9, 16, 16, 16, 9, 11, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000533956639 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639 Building ZINC000533956639 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000533956639 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 592) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2Cl)c2ccc(OC)cc2OC)cn1) `ZINC000533956639.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000533956639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000533956639 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2Cl)c2ccc(OC)cc2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 7, 7, 6, 7, 7, 7, 6, 9, 9, 6, 9, 17, 9, 9, 9, 12, 6, 6, 16, 16, 16, 16, 16, 6, 4, 7, 7, 6, 7, 9, 9, 17, 17, 17, 9, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 593) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2Cl)c2ccc(OC)cc2OC)cn1) `ZINC000533956639.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000533956639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000533956639 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2Cl)c2ccc(OC)cc2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 7, 7, 6, 7, 7, 7, 6, 9, 9, 6, 9, 16, 9, 9, 9, 11, 6, 6, 15, 15, 15, 15, 15, 6, 4, 7, 7, 6, 7, 9, 9, 16, 16, 16, 9, 11, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000533956639 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533956639 Building ZINC000606810260 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000606810260 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/594 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(Br)cc2)sc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000606810260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000606810260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000606810260 none Cc1nc(c2ccc(Br)cc2)sc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 36, 36, 36, 36, 36, 36, 23, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 23, 23, 23, 36, 36, 36, 36, 8, 8, 8, 4, 10, 10, 10, 10, 10] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/595 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/595' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(Br)cc2)sc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000606810260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000606810260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000606810260 none Cc1nc(c2ccc(Br)cc2)sc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 28, 28, 28, 28, 28, 28, 22, 9, 5, 9, 9, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 22, 22, 22, 28, 28, 28, 28, 9, 9, 9, 5, 10, 10, 10, 10, 10] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000606810260 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260 Building ZINC000606810260 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000606810260 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 594) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/594: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(Br)cc2)sc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000606810260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000606810260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000606810260 none Cc1nc(c2ccc(Br)cc2)sc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 36, 36, 36, 36, 36, 36, 23, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 23, 23, 23, 36, 36, 36, 36, 8, 8, 8, 4, 10, 10, 10, 10, 10] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 595) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(Br)cc2)sc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000606810260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000606810260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000606810260 none Cc1nc(c2ccc(Br)cc2)sc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 28, 28, 28, 28, 28, 28, 22, 9, 5, 9, 9, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 22, 22, 22, 28, 28, 28, 28, 9, 9, 9, 5, 10, 10, 10, 10, 10] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000606810260 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810260 Building ZINC000606810261 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000606810261 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/596 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(Br)cc2)sc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000606810261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000606810261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000606810261 none Cc1nc(c2ccc(Br)cc2)sc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 31, 31, 31, 31, 31, 31, 24, 9, 5, 9, 9, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 24, 24, 24, 31, 31, 31, 31, 9, 9, 9, 5, 10, 10, 10, 10, 10] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/597 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/597' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(Br)cc2)sc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000606810261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000606810261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000606810261 none Cc1nc(c2ccc(Br)cc2)sc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 35, 35, 35, 35, 35, 35, 22, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 22, 22, 22, 35, 35, 35, 35, 8, 8, 8, 4, 10, 10, 10, 10, 10] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000606810261 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261 Building ZINC000606810261 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000606810261 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 596) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(Br)cc2)sc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000606810261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000606810261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000606810261 none Cc1nc(c2ccc(Br)cc2)sc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 31, 31, 31, 31, 31, 31, 24, 9, 5, 9, 9, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 24, 24, 24, 31, 31, 31, 31, 9, 9, 9, 5, 10, 10, 10, 10, 10] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 597) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(Br)cc2)sc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000606810261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000606810261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000606810261 none Cc1nc(c2ccc(Br)cc2)sc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 35, 35, 35, 35, 35, 35, 22, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 22, 22, 22, 35, 35, 35, 35, 8, 8, 8, 4, 10, 10, 10, 10, 10] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000606810261 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606810261 Building ZINC000606825989 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000606825989 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/598 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccc(C#N)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1C) `ZINC000606825989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000606825989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000606825989 none Cc1nn(c2ccc(C#N)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 26, 26, 20, 20, 20, 26, 26, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 20, 20, 20, 20, 20, 26, 26, 26, 26, 5, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 20, 20, 20] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 96 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/599 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/599' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccc(C#N)cc2)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1C) `ZINC000606825989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000606825989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000606825989 none Cc1nn(c2ccc(C#N)cc2)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 26, 26, 20, 25, 26, 26, 26, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 20, 20, 20, 20, 20, 26, 26, 26, 26, 5, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 20, 20, 20] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 97 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000606825989 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989 Building ZINC000606825989 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000606825989 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 598) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/598: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccc(C#N)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1C) `ZINC000606825989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000606825989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000606825989 none Cc1nn(c2ccc(C#N)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 26, 26, 20, 20, 20, 26, 26, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 20, 20, 20, 20, 20, 26, 26, 26, 26, 5, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 20, 20, 20] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 96 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 599) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/599: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccc(C#N)cc2)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1C) `ZINC000606825989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000606825989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000606825989 none Cc1nn(c2ccc(C#N)cc2)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 26, 26, 20, 25, 26, 26, 26, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 20, 20, 20, 20, 20, 26, 26, 26, 26, 5, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 20, 20, 20] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 97 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000606825989 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000606825989 Building ZINC000607052517 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607052517 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/600 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CN2CCCC2)C1) `ZINC000607052517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607052517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000607052517 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CN2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 11, 14, 14, 14, 14, 3, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 3, 3, 3, 3, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 74 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/601 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/601' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CN2CCCC2)C1) `ZINC000607052517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607052517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000607052517 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CN2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 14, 14, 3, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 10, 15, 15, 15, 15, 3, 2, 2, 2, 14, 14, 8, 14, 2, 2, 2, 3, 3, 3, 3, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 79 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607052517 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517 Building ZINC000607052517 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607052517 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 600) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/600: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CN2CCCC2)C1) `ZINC000607052517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607052517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000607052517 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CN2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 11, 14, 14, 14, 14, 3, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 3, 3, 3, 3, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 74 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 601) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/601: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CN2CCCC2)C1) `ZINC000607052517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607052517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000607052517 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CN2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 14, 14, 3, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 10, 15, 15, 15, 15, 3, 2, 2, 2, 14, 14, 8, 14, 2, 2, 2, 3, 3, 3, 3, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 79 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607052517 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052517 Building ZINC000607052518 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607052518 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/602 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CN2CCCC2)C1) `ZINC000607052518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607052518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000607052518 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CN2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 10, 15, 15, 15, 15, 3, 2, 2, 2, 13, 13, 2, 13, 2, 2, 2, 3, 3, 3, 3, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 68 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/603 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](CN2CCCC2)C1) `ZINC000607052518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607052518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000607052518 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](CN2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 11, 14, 14, 14, 14, 3, 3, 3, 3, 18, 18, 3, 18, 3, 3, 3, 3, 3, 3, 3, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 81 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607052518 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518 Building ZINC000607052518 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607052518 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 602) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/602: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CN2CCCC2)C1) `ZINC000607052518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607052518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000607052518 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CN2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 10, 15, 15, 15, 15, 3, 2, 2, 2, 13, 13, 2, 13, 2, 2, 2, 3, 3, 3, 3, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 68 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 603) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/603: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](CN2CCCC2)C1) `ZINC000607052518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607052518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000607052518 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](CN2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 11, 14, 14, 14, 14, 3, 3, 3, 3, 18, 18, 3, 18, 3, 3, 3, 3, 3, 3, 3, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 81 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607052518 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607052518 Building ZINC000607053064 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607053064 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/604 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000607053064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607053064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607053064 none CC[C@H](C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 10, 10, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 33, 5, 5, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 150 rigid atoms, others: [8, 9, 10, 11, 12, 45, 14, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/605 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000607053064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607053064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607053064 none CC[C@H](C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 10, 10, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 33, 7, 7, 1, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3] 150 rigid atoms, others: [8, 9, 10, 11, 12, 45, 14, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607053064 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064 Building ZINC000607053064 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607053064 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 604) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/604: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000607053064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607053064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607053064 none CC[C@H](C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 10, 10, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 33, 5, 5, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 150 rigid atoms, others: [8, 9, 10, 11, 12, 45, 14, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 605) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/605: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000607053064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607053064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607053064 none CC[C@H](C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 10, 10, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 33, 7, 7, 1, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3] 150 rigid atoms, others: [8, 9, 10, 11, 12, 45, 14, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607053064 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053064 Building ZINC000607053065 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607053065 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/606 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000607053065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607053065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607053065 none CC[C@@H](C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 7, 10, 10, 4, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 7, 7, 7, 21, 4, 4, 1, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 150 rigid atoms, others: [8, 9, 10, 11, 12, 45, 14, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 86 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/607 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000607053065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607053065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607053065 none CC[C@@H](C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 8, 11, 10, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 4, 10, 10, 10, 10, 10, 10, 2, 2, 11, 11, 11, 11, 11, 11, 10, 11, 8, 8, 8, 24, 5, 5, 2, 2, 2, 2, 10, 10, 6, 10, 2, 2, 2] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607053065 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065 Building ZINC000607053065 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607053065 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 606) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/606: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000607053065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607053065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607053065 none CC[C@@H](C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 7, 10, 10, 4, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 7, 7, 7, 21, 4, 4, 1, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 150 rigid atoms, others: [8, 9, 10, 11, 12, 45, 14, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 86 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 607) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/607: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000607053065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607053065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607053065 none CC[C@@H](C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 8, 11, 10, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 4, 10, 10, 10, 10, 10, 10, 2, 2, 11, 11, 11, 11, 11, 11, 10, 11, 8, 8, 8, 24, 5, 5, 2, 2, 2, 2, 10, 10, 6, 10, 2, 2, 2] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607053065 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053065 Building ZINC000607053066 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607053066 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/608 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000607053066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607053066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607053066 none CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 9, 9, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 33, 6, 6, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 150 rigid atoms, others: [8, 9, 10, 11, 12, 45, 14, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 106 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/609 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000607053066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607053066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607053066 none CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 10, 10, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 33, 5, 5, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 150 rigid atoms, others: [8, 9, 10, 11, 12, 45, 14, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607053066 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066 Building ZINC000607053066 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607053066 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 608) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/608: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000607053066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607053066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607053066 none CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 9, 9, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 33, 6, 6, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 150 rigid atoms, others: [8, 9, 10, 11, 12, 45, 14, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 106 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 609) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/609: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000607053066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607053066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607053066 none CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 10, 10, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 33, 5, 5, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 150 rigid atoms, others: [8, 9, 10, 11, 12, 45, 14, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607053066 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053066 Building ZINC000607053067 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607053067 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/610 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000607053067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607053067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607053067 none CC[C@H](C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 10, 10, 12, 7, 12, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 36, 7, 7, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 113 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/611 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/611' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000607053067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607053067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607053067 none CC[C@H](C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 6, 9, 9, 3, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 18, 3, 3, 1, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 150 rigid atoms, others: [8, 9, 10, 11, 12, 45, 14, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 80 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607053067 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067 Building ZINC000607053067 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607053067 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 610) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000607053067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607053067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607053067 none CC[C@H](C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 10, 10, 12, 7, 12, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 36, 7, 7, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 113 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 611) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/611: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000607053067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607053067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607053067 none CC[C@H](C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 6, 9, 9, 3, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 18, 3, 3, 1, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 150 rigid atoms, others: [8, 9, 10, 11, 12, 45, 14, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 80 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607053067 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607053067 Building ZINC000607320890 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607320890 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/612 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2CCO[C@@H]2C1(C)C) `ZINC000607320890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607320890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000607320890 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2CCO[C@@H]2C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/613 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/613' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2CCO[C@@H]2C1(C)C) `ZINC000607320890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607320890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000607320890 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2CCO[C@@H]2C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 12, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 16, 16, 12, 16, 3, 3, 3, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 64 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607320890 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890 Building ZINC000607320890 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607320890 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 612) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/612: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2CCO[C@@H]2C1(C)C) `ZINC000607320890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607320890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000607320890 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2CCO[C@@H]2C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 613) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/613: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2CCO[C@@H]2C1(C)C) `ZINC000607320890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607320890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000607320890 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2CCO[C@@H]2C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 12, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 16, 16, 12, 16, 3, 3, 3, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 64 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607320890 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320890 Building ZINC000607320891 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607320891 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/614 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2CCO[C@H]2C1(C)C) `ZINC000607320891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607320891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000607320891 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2CCO[C@H]2C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 21, 21, 4, 21, 4, 4, 4, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/615 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/615' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2CCO[C@H]2C1(C)C) `ZINC000607320891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607320891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000607320891 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2CCO[C@H]2C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 17, 17, 4, 17, 17, 17, 17, 17, 17, 4, 4, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 17, 17, 4, 17, 4, 4, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607320891 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891 Building ZINC000607320891 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607320891 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 614) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2CCO[C@H]2C1(C)C) `ZINC000607320891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607320891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000607320891 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2CCO[C@H]2C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 21, 21, 4, 21, 4, 4, 4, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 615) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2CCO[C@H]2C1(C)C) `ZINC000607320891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607320891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000607320891 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@@H]2CCO[C@H]2C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 17, 17, 4, 17, 17, 17, 17, 17, 17, 4, 4, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 17, 17, 4, 17, 4, 4, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607320891 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320891 Building ZINC000607320892 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607320892 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/616 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CCO[C@@H]2C1(C)C) `ZINC000607320892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607320892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' Warning: atom stereo specified for planar atom 17 Warning: atom stereo specified for planar atom 17 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000607320892 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CCO[C@@H]2C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 25, 25, 6, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 25, 25, 14, 25, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 99 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/617 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CCO[C@@H]2C1(C)C) `ZINC000607320892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607320892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' Warning: atom stereo specified for planar atom 17 Warning: atom stereo specified for planar atom 17 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000607320892 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CCO[C@@H]2C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 21, 21, 3, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 21, 21, 10, 21, 3, 3, 3, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 87 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607320892 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892 Building ZINC000607320892 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607320892 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 616) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CCO[C@@H]2C1(C)C) `ZINC000607320892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607320892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' Warning: atom stereo specified for planar atom 17 Warning: atom stereo specified for planar atom 17 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000607320892 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CCO[C@@H]2C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 25, 25, 6, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 25, 25, 14, 25, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 99 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 617) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CCO[C@@H]2C1(C)C) `ZINC000607320892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607320892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' Warning: atom stereo specified for planar atom 17 Warning: atom stereo specified for planar atom 17 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000607320892 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CCO[C@@H]2C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 21, 21, 3, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 21, 21, 10, 21, 3, 3, 3, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 87 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607320892 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320892 Building ZINC000607320878 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607320878 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/618 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CCO[C@H]2C1(C)C) `ZINC000607320878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607320878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000607320878 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CCO[C@H]2C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 20, 20, 12, 20, 20, 20, 20, 20, 20, 4, 4, 1, 1, 1, 1, 3, 3, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 20, 20, 20, 20, 4, 4, 4, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 83 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/619 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CCO[C@H]2C1(C)C) `ZINC000607320878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607320878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000607320878 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CCO[C@H]2C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 20, 20, 14, 20, 20, 20, 20, 20, 20, 4, 4, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 20, 20, 14, 20, 4, 4, 4, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 67 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607320878 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878 Building ZINC000607320878 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607320878 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 618) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/618: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CCO[C@H]2C1(C)C) `ZINC000607320878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607320878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000607320878 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CCO[C@H]2C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 20, 20, 12, 20, 20, 20, 20, 20, 20, 4, 4, 1, 1, 1, 1, 3, 3, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 20, 20, 20, 20, 4, 4, 4, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 83 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 619) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/619: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CCO[C@H]2C1(C)C) `ZINC000607320878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607320878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000607320878 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CCO[C@H]2C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 20, 20, 14, 20, 20, 20, 20, 20, 20, 4, 4, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 20, 20, 14, 20, 4, 4, 4, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 67 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607320878 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607320878 Building ZINC000607330971 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607330971 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/620 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(Oc2ncccc2CNC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1) `ZINC000607330971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607330971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000607330971 none COc1cccc(Oc2ncccc2CNC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 22, 22, 22, 22, 22, 22, 22, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 22, 22, 22, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 29] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/621 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/621' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(Oc2ncccc2CNC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1) `ZINC000607330971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607330971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000607330971 none COc1cccc(Oc2ncccc2CNC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 22, 22, 22, 22, 22, 22, 22, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 22, 22, 22, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 30] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607330971 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971 Building ZINC000607330971 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607330971 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 620) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(Oc2ncccc2CNC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1) `ZINC000607330971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607330971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000607330971 none COc1cccc(Oc2ncccc2CNC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 22, 22, 22, 22, 22, 22, 22, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 22, 22, 22, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 29] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 621) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(Oc2ncccc2CNC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1) `ZINC000607330971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607330971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000607330971 none COc1cccc(Oc2ncccc2CNC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 22, 22, 22, 22, 22, 22, 22, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 22, 22, 22, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 30] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607330971 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607330971 Building ZINC000607556249 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000607556249 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/622 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000607556249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607556249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000607556249 none C[N@]1CC[N@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 38, 37, 38, 38, 38, 38, 38, 38, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 15, 15, 4, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/623 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000607556249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607556249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000607556249 none C[N@]1CC[N@@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 38, 23, 38, 38, 38, 38, 38, 38, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 15, 15, 4, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/624 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/624' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000607556249.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000607556249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000607556249 none C[N@]1CC[N@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 39, 39, 39, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 16, 16, 4, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/625 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/625' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000607556249.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000607556249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000607556249 none C[N@]1CC[N@@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 38, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 15, 15, 4, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607556249 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 Building ZINC000607556249 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000607556249 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 622) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/622: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000607556249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607556249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000607556249 none C[N@]1CC[N@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 38, 37, 38, 38, 38, 38, 38, 38, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 15, 15, 4, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 623) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000607556249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607556249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000607556249 none C[N@]1CC[N@@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 38, 23, 38, 38, 38, 38, 38, 38, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 15, 15, 4, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 624) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000607556249.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000607556249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000607556249 none C[N@]1CC[N@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 39, 39, 39, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 16, 16, 4, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 625) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000607556249.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000607556249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000607556249 none C[N@]1CC[N@@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 38, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 15, 15, 4, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607556249 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 Building ZINC000607556249 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000607556249 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 622) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/622: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000607556249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607556249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000607556249 none C[N@]1CC[N@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 38, 37, 38, 38, 38, 38, 38, 38, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 15, 15, 4, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 623) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000607556249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607556249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000607556249 none C[N@]1CC[N@@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 38, 23, 38, 38, 38, 38, 38, 38, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 15, 15, 4, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 624) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000607556249.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000607556249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000607556249 none C[N@]1CC[N@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 39, 39, 39, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 16, 16, 4, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 625) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000607556249.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000607556249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000607556249 none C[N@]1CC[N@@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 38, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 15, 15, 4, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607556249 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 Building ZINC000607556249 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000607556249 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 622) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/622: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000607556249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607556249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000607556249 none C[N@]1CC[N@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 38, 37, 38, 38, 38, 38, 38, 38, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 15, 15, 4, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 623) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000607556249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607556249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000607556249 none C[N@]1CC[N@@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 38, 23, 38, 38, 38, 38, 38, 38, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 15, 15, 4, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 624) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000607556249.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000607556249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000607556249 none C[N@]1CC[N@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 39, 39, 39, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 16, 16, 4, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 625) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000607556249.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000607556249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000607556249 none C[N@]1CC[N@@](c2ccc(C(F)(F)F)cc2CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 38, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 15, 15, 4, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607556249 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607556249 Building ZINC000607668534 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000607668534 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/626 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000607668534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607668534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607668534 none CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 21, 33, 33, 33, 33, 33, 17, 12, 17, 11, 17, 17, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 33, 33, 33, 33, 33, 20, 20, 17, 11, 17, 17, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/627 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000607668534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607668534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607668534 none CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 21, 33, 33, 33, 33, 33, 17, 12, 17, 11, 17, 17, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 33, 33, 33, 33, 33, 20, 20, 17, 11, 17, 17, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/628 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/628' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000607668534.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000607668534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607668534 none CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 36, 36, 36, 36, 36, 18, 13, 18, 12, 18, 18, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 36, 36, 36, 36, 36, 23, 23, 18, 12, 18, 18, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/629 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/629' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000607668534.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000607668534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607668534 none CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 36, 36, 36, 36, 36, 18, 13, 18, 12, 18, 18, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 36, 36, 36, 36, 36, 23, 23, 18, 12, 18, 18, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607668534 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 Building ZINC000607668534 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000607668534 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 626) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/626: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000607668534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607668534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607668534 none CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 21, 33, 33, 33, 33, 33, 17, 12, 17, 11, 17, 17, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 33, 33, 33, 33, 33, 20, 20, 17, 11, 17, 17, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 627) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000607668534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607668534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607668534 none CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 21, 33, 33, 33, 33, 33, 17, 12, 17, 11, 17, 17, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 33, 33, 33, 33, 33, 20, 20, 17, 11, 17, 17, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 628) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000607668534.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000607668534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607668534 none CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 36, 36, 36, 36, 36, 18, 13, 18, 12, 18, 18, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 36, 36, 36, 36, 36, 23, 23, 18, 12, 18, 18, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 629) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/629: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000607668534.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000607668534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607668534 none CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 36, 36, 36, 36, 36, 18, 13, 18, 12, 18, 18, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 36, 36, 36, 36, 36, 23, 23, 18, 12, 18, 18, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607668534 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 Building ZINC000607668534 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000607668534 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 626) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/626: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000607668534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607668534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607668534 none CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 21, 33, 33, 33, 33, 33, 17, 12, 17, 11, 17, 17, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 33, 33, 33, 33, 33, 20, 20, 17, 11, 17, 17, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 627) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000607668534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607668534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607668534 none CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 21, 33, 33, 33, 33, 33, 17, 12, 17, 11, 17, 17, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 33, 33, 33, 33, 33, 20, 20, 17, 11, 17, 17, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 628) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000607668534.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000607668534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607668534 none CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 36, 36, 36, 36, 36, 18, 13, 18, 12, 18, 18, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 36, 36, 36, 36, 36, 23, 23, 18, 12, 18, 18, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 629) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/629: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000607668534.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000607668534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607668534 none CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 36, 36, 36, 36, 36, 18, 13, 18, 12, 18, 18, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 36, 36, 36, 36, 36, 23, 23, 18, 12, 18, 18, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607668534 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 Building ZINC000607668534 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000607668534 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 626) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/626: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000607668534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607668534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607668534 none CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 21, 33, 33, 33, 33, 33, 17, 12, 17, 11, 17, 17, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 33, 33, 33, 33, 33, 20, 20, 17, 11, 17, 17, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 627) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000607668534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607668534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607668534 none CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 21, 33, 33, 33, 33, 33, 17, 12, 17, 11, 17, 17, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 33, 33, 33, 33, 33, 20, 20, 17, 11, 17, 17, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 628) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000607668534.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000607668534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607668534 none CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 36, 36, 36, 36, 36, 18, 13, 18, 12, 18, 18, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 36, 36, 36, 36, 36, 23, 23, 18, 12, 18, 18, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 629) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/629: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000607668534.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000607668534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000607668534 none CN(Cc1ccco1)Cc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 36, 36, 36, 36, 36, 18, 13, 18, 12, 18, 18, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 36, 36, 36, 36, 36, 23, 23, 18, 12, 18, 18, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000607668534 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000607668534 Building ZINC000533974637 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000533974637 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/630 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)cn1) `ZINC000533974637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000533974637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000533974637 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 16, 16, 16, 25, 25, 16, 16, 25, 25, 16, 16, 4, 4, 8, 8, 8, 8, 8, 4, 2, 3, 3, 3, 25, 25, 25, 25, 16, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/631 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/631' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)cn1) `ZINC000533974637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000533974637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000533974637 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 16, 16, 16, 30, 30, 16, 16, 30, 30, 16, 16, 3, 3, 9, 9, 9, 9, 9, 3, 2, 2, 2, 2, 30, 30, 30, 30, 16, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000533974637 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637 Building ZINC000533974637 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000533974637 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 630) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/630: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)cn1) `ZINC000533974637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000533974637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000533974637 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 16, 16, 16, 25, 25, 16, 16, 25, 25, 16, 16, 4, 4, 8, 8, 8, 8, 8, 4, 2, 3, 3, 3, 25, 25, 25, 25, 16, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 631) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/631: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)cn1) `ZINC000533974637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000533974637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000533974637 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 16, 16, 16, 30, 30, 16, 16, 30, 30, 16, 16, 3, 3, 9, 9, 9, 9, 9, 3, 2, 2, 2, 2, 30, 30, 30, 30, 16, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000533974637 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974637 Building ZINC000533974638 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000533974638 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/632 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)cn1) `ZINC000533974638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000533974638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000533974638 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 16, 16, 16, 29, 29, 16, 18, 29, 29, 16, 16, 3, 3, 9, 9, 9, 9, 9, 3, 2, 2, 2, 2, 29, 29, 29, 29, 16, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/633 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)cn1) `ZINC000533974638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000533974638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000533974638 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 16, 16, 16, 25, 25, 16, 16, 25, 25, 16, 16, 4, 4, 8, 8, 8, 8, 8, 4, 2, 3, 3, 3, 25, 25, 25, 25, 16, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000533974638 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638 Building ZINC000533974638 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000533974638 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 632) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/632: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)cn1) `ZINC000533974638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000533974638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000533974638 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 16, 16, 16, 29, 29, 16, 18, 29, 29, 16, 16, 3, 3, 9, 9, 9, 9, 9, 3, 2, 2, 2, 2, 29, 29, 29, 29, 16, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 633) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/633: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)cn1) `ZINC000533974638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000533974638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000533974638 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 16, 16, 16, 25, 25, 16, 16, 25, 25, 16, 16, 4, 4, 8, 8, 8, 8, 8, 4, 2, 3, 3, 3, 25, 25, 25, 25, 16, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000533974638 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533974638 Building ZINC000608488605 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608488605 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/634 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(CC2CC2)c1) `ZINC000608488605.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608488605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000608488605 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(CC2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 10, 10, 10, 6, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 2, 6, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/635 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(CC2CC2)c1) `ZINC000608488605.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608488605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000608488605 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(CC2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 10, 10, 10, 5, 3, 3, 3, 11, 11, 6, 11, 3, 3, 3, 2, 5, 10, 10, 10, 10, 10, 10, 10, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000608488605 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605 Building ZINC000608488605 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608488605 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 634) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(CC2CC2)c1) `ZINC000608488605.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608488605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000608488605 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(CC2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 10, 10, 10, 6, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 2, 6, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 635) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(CC2CC2)c1) `ZINC000608488605.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608488605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000608488605 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(CC2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 10, 10, 10, 5, 3, 3, 3, 11, 11, 6, 11, 3, 3, 3, 2, 5, 10, 10, 10, 10, 10, 10, 10, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000608488605 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608488605 Building ZINC000608895855 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608895855 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/636 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(OC(F)(F)F)cc1) `ZINC000608895855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608895855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000608895855 none COC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(OC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 9, 22, 4, 3, 4, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 4, 4, 4, 4, 4, 26, 30, 30, 30, 4, 4, 22, 22, 22, 9, 9, 3, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/637 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(OC(F)(F)F)cc1) `ZINC000608895855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608895855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000608895855 none COC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(OC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 9, 22, 4, 2, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 4, 4, 4, 26, 26, 26, 26, 4, 4, 22, 22, 22, 9, 9, 2, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000608895855 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855 Building ZINC000608895855 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608895855 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 636) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(OC(F)(F)F)cc1) `ZINC000608895855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608895855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000608895855 none COC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(OC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 9, 22, 4, 3, 4, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 4, 4, 4, 4, 4, 26, 30, 30, 30, 4, 4, 22, 22, 22, 9, 9, 3, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 637) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(OC(F)(F)F)cc1) `ZINC000608895855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608895855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000608895855 none COC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(OC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 9, 22, 4, 2, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 4, 4, 4, 26, 26, 26, 26, 4, 4, 22, 22, 22, 9, 9, 2, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000608895855 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895855 Building ZINC000608895856 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608895856 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/638 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(OC(F)(F)F)cc1) `ZINC000608895856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608895856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000608895856 none COC(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(OC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 9, 22, 4, 2, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 4, 4, 4, 4, 4, 26, 26, 26, 26, 4, 4, 22, 22, 22, 9, 9, 2, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/639 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/639' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(OC(F)(F)F)cc1) `ZINC000608895856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608895856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000608895856 none COC(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(OC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 9, 22, 4, 3, 4, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 4, 4, 4, 26, 30, 30, 30, 4, 4, 22, 22, 22, 9, 9, 3, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000608895856 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856 Building ZINC000608895856 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608895856 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 638) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(OC(F)(F)F)cc1) `ZINC000608895856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608895856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000608895856 none COC(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(OC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 9, 22, 4, 2, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 4, 4, 4, 4, 4, 26, 26, 26, 26, 4, 4, 22, 22, 22, 9, 9, 2, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 639) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(OC(F)(F)F)cc1) `ZINC000608895856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608895856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000608895856 none COC(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(OC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 9, 22, 4, 3, 4, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 4, 4, 4, 26, 30, 30, 30, 4, 4, 22, 22, 22, 9, 9, 3, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000608895856 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000608895856 Building ZINC000533993633 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000533993633 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/640 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(F)c2)c2cccc(Br)c2)cn1) `ZINC000533993633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000533993633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000533993633 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(F)c2)c2cccc(Br)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 11, 11, 11, 11, 11, 11, 4, 9, 9, 9, 9, 9, 9, 5, 5, 9, 9, 9, 9, 9, 5, 2, 11, 11, 11, 11, 9, 9, 9, 9, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/641 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(F)c2)c2cccc(Br)c2)cn1) `ZINC000533993633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000533993633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000533993633 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(F)c2)c2cccc(Br)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 9, 9, 9, 9, 9, 4, 11, 11, 8, 11, 11, 11, 5, 5, 9, 9, 9, 9, 9, 5, 2, 9, 9, 9, 9, 11, 11, 11, 11, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000533993633 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633 Building ZINC000533993633 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000533993633 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 640) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(F)c2)c2cccc(Br)c2)cn1) `ZINC000533993633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000533993633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000533993633 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(F)c2)c2cccc(Br)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 11, 11, 11, 11, 11, 11, 4, 9, 9, 9, 9, 9, 9, 5, 5, 9, 9, 9, 9, 9, 5, 2, 11, 11, 11, 11, 9, 9, 9, 9, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 641) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(F)c2)c2cccc(Br)c2)cn1) `ZINC000533993633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000533993633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000533993633 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(F)c2)c2cccc(Br)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 9, 9, 9, 9, 9, 4, 11, 11, 8, 11, 11, 11, 5, 5, 9, 9, 9, 9, 9, 5, 2, 9, 9, 9, 9, 11, 11, 11, 11, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000533993633 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993633 Building ZINC000533993634 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000533993634 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/642 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](c2cccc(F)c2)c2cccc(Br)c2)cn1) `ZINC000533993634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000533993634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000533993634 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](c2cccc(F)c2)c2cccc(Br)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 9, 9, 9, 9, 9, 4, 11, 11, 8, 11, 11, 11, 5, 5, 9, 9, 9, 9, 9, 5, 2, 9, 9, 9, 9, 11, 11, 10, 11, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/643 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/643' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](c2cccc(F)c2)c2cccc(Br)c2)cn1) `ZINC000533993634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000533993634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000533993634 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](c2cccc(F)c2)c2cccc(Br)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 11, 11, 11, 11, 11, 11, 4, 9, 9, 9, 9, 9, 9, 5, 5, 9, 9, 9, 9, 9, 5, 2, 11, 11, 11, 11, 9, 9, 9, 9, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000533993634 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634 Building ZINC000533993634 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000533993634 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 642) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/642: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](c2cccc(F)c2)c2cccc(Br)c2)cn1) `ZINC000533993634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000533993634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000533993634 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](c2cccc(F)c2)c2cccc(Br)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 9, 9, 9, 9, 9, 4, 11, 11, 8, 11, 11, 11, 5, 5, 9, 9, 9, 9, 9, 5, 2, 9, 9, 9, 9, 11, 11, 10, 11, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 643) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](c2cccc(F)c2)c2cccc(Br)c2)cn1) `ZINC000533993634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000533993634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000533993634 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](c2cccc(F)c2)c2cccc(Br)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 11, 11, 11, 11, 11, 11, 4, 9, 9, 9, 9, 9, 9, 5, 5, 9, 9, 9, 9, 9, 5, 2, 11, 11, 11, 11, 9, 9, 9, 9, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000533993634 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000533993634 Building ZINC000534010666 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534010666 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/644 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccc(OC)cc2)CCCC3)cn1) `ZINC000534010666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534010666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000534010666 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccc(OC)cc2)CCCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 18, 10, 10, 8, 8, 8, 8, 6, 6, 13, 13, 13, 13, 13, 6, 3, 10, 10, 18, 18, 18, 10, 10, 8, 8, 8, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/645 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccc(OC)cc2)CCCC3)cn1) `ZINC000534010666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534010666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000534010666 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccc(OC)cc2)CCCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 19, 11, 11, 7, 7, 7, 7, 6, 6, 17, 17, 17, 17, 17, 6, 3, 11, 11, 19, 19, 19, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534010666 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666 Building ZINC000534010666 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534010666 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 644) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccc(OC)cc2)CCCC3)cn1) `ZINC000534010666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534010666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000534010666 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccc(OC)cc2)CCCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 18, 10, 10, 8, 8, 8, 8, 6, 6, 13, 13, 13, 13, 13, 6, 3, 10, 10, 18, 18, 18, 10, 10, 8, 8, 8, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 645) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/645: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccc(OC)cc2)CCCC3)cn1) `ZINC000534010666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534010666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000534010666 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccc(OC)cc2)CCCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 19, 11, 11, 7, 7, 7, 7, 6, 6, 17, 17, 17, 17, 17, 6, 3, 11, 11, 19, 19, 19, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534010666 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010666 Building ZINC000534010464 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534010464 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/646 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(c2ccc(OC)cc2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000534010464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534010464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000534010464 none CCOC(=O)c1sc(c2ccc(OC)cc2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 8, 4, 8, 4, 4, 4, 4, 15, 15, 4, 4, 23, 15, 15, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 5, 13, 13, 13, 13, 13, 15, 15, 23, 23, 23, 15, 15, 4, 2, 5, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/647 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/647' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(c2ccc(OC)cc2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000534010464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534010464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000534010464 none CCOC(=O)c1sc(c2ccc(OC)cc2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 4, 8, 4, 4, 4, 4, 15, 15, 4, 4, 25, 15, 15, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 5, 11, 11, 11, 11, 11, 15, 15, 25, 25, 25, 15, 15, 4, 2, 5, 11, 11, 11, 11, 11, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534010464 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464 Building ZINC000534010464 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534010464 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 646) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/646: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(c2ccc(OC)cc2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000534010464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534010464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000534010464 none CCOC(=O)c1sc(c2ccc(OC)cc2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 8, 4, 8, 4, 4, 4, 4, 15, 15, 4, 4, 23, 15, 15, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 5, 13, 13, 13, 13, 13, 15, 15, 23, 23, 23, 15, 15, 4, 2, 5, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 647) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/647: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(c2ccc(OC)cc2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000534010464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534010464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000534010464 none CCOC(=O)c1sc(c2ccc(OC)cc2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 4, 8, 4, 4, 4, 4, 15, 15, 4, 4, 25, 15, 15, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 5, 11, 11, 11, 11, 11, 15, 15, 25, 25, 25, 15, 15, 4, 2, 5, 11, 11, 11, 11, 11, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534010464 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534010464 Building ZINC000534220075 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000534220075 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/648 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000534220075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534220075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000534220075 none O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 9, 9, 9, 9, 9, 9, 9, 29, 35, 35, 32, 35, 35, 9, 9, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 29, 29, 35, 35, 35, 35, 35, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/649 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/649' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000534220075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534220075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000534220075 none O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 9, 9, 9, 9, 9, 9, 9, 29, 35, 35, 32, 35, 35, 9, 9, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 29, 29, 35, 35, 35, 35, 35, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/650 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/650' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000534220075.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000534220075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000534220075 none O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 8, 8, 8, 8, 8, 8, 8, 24, 33, 33, 28, 33, 33, 8, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 24, 24, 33, 33, 33, 33, 33, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/651 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/651' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000534220075.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000534220075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000534220075 none O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 8, 8, 8, 8, 8, 8, 8, 24, 33, 33, 28, 33, 33, 8, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 24, 24, 33, 33, 33, 33, 33, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534220075 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 Building ZINC000534220075 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000534220075 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 648) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/648: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000534220075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534220075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000534220075 none O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 9, 9, 9, 9, 9, 9, 9, 29, 35, 35, 32, 35, 35, 9, 9, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 29, 29, 35, 35, 35, 35, 35, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 649) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/649: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000534220075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534220075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000534220075 none O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 9, 9, 9, 9, 9, 9, 9, 29, 35, 35, 32, 35, 35, 9, 9, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 29, 29, 35, 35, 35, 35, 35, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 650) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/650: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000534220075.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000534220075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000534220075 none O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 8, 8, 8, 8, 8, 8, 8, 24, 33, 33, 28, 33, 33, 8, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 24, 24, 33, 33, 33, 33, 33, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 651) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/651: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000534220075.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000534220075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000534220075 none O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 8, 8, 8, 8, 8, 8, 8, 24, 33, 33, 28, 33, 33, 8, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 24, 24, 33, 33, 33, 33, 33, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534220075 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 Building ZINC000534220075 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000534220075 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 648) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/648: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000534220075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534220075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000534220075 none O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 9, 9, 9, 9, 9, 9, 9, 29, 35, 35, 32, 35, 35, 9, 9, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 29, 29, 35, 35, 35, 35, 35, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 649) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/649: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000534220075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534220075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000534220075 none O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 9, 9, 9, 9, 9, 9, 9, 29, 35, 35, 32, 35, 35, 9, 9, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 29, 29, 35, 35, 35, 35, 35, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 650) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/650: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000534220075.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000534220075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000534220075 none O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 8, 8, 8, 8, 8, 8, 8, 24, 33, 33, 28, 33, 33, 8, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 24, 24, 33, 33, 33, 33, 33, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 651) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/651: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000534220075.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000534220075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000534220075 none O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 8, 8, 8, 8, 8, 8, 8, 24, 33, 33, 28, 33, 33, 8, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 24, 24, 33, 33, 33, 33, 33, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534220075 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 Building ZINC000534220075 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000534220075 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 648) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/648: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000534220075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534220075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000534220075 none O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 9, 9, 9, 9, 9, 9, 9, 29, 35, 35, 32, 35, 35, 9, 9, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 29, 29, 35, 35, 35, 35, 35, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 649) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/649: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000534220075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534220075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000534220075 none O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 9, 9, 9, 9, 9, 9, 9, 29, 35, 35, 32, 35, 35, 9, 9, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 29, 29, 35, 35, 35, 35, 35, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 650) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/650: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000534220075.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000534220075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000534220075 none O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 8, 8, 8, 8, 8, 8, 8, 24, 33, 33, 28, 33, 33, 8, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 24, 24, 33, 33, 33, 33, 33, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 651) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/651: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000534220075.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000534220075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000534220075 none O=C(N1CCC2(CCN(Cc3ccccc3)C2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 8, 8, 8, 8, 8, 8, 8, 24, 33, 33, 28, 33, 33, 8, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 24, 24, 33, 33, 33, 33, 33, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534220075 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534220075 Building ZINC000534458093 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534458093 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/652 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cn1cnc2ccccc21) `ZINC000534458093.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534458093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000534458093 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cn1cnc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 15, 32, 32, 32, 32, 32, 32, 32, 32, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 9, 9, 9, 9, 9, 9, 15, 15, 32, 32, 32, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 106 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/653 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cn1cnc2ccccc21) `ZINC000534458093.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534458093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000534458093 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cn1cnc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 16, 34, 34, 34, 34, 34, 34, 34, 34, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 8, 8, 8, 8, 8, 8, 16, 16, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 110 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534458093 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093 Building ZINC000534458093 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534458093 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 652) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/652: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cn1cnc2ccccc21) `ZINC000534458093.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534458093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000534458093 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cn1cnc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 15, 32, 32, 32, 32, 32, 32, 32, 32, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 9, 9, 9, 9, 9, 9, 15, 15, 32, 32, 32, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 106 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 653) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/653: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cn1cnc2ccccc21) `ZINC000534458093.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534458093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000534458093 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cn1cnc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 16, 34, 34, 34, 34, 34, 34, 34, 34, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 8, 8, 8, 8, 8, 8, 16, 16, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 110 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534458093 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458093 Building ZINC000534458094 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534458094 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/654 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cn1cnc2ccccc21) `ZINC000534458094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534458094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000534458094 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cn1cnc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 17, 32, 32, 32, 32, 32, 32, 32, 32, 3, 3, 3, 8, 8, 4, 8, 8, 3, 3, 3, 9, 9, 9, 9, 9, 9, 17, 17, 32, 32, 32, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 105 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/655 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/655' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cn1cnc2ccccc21) `ZINC000534458094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534458094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000534458094 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cn1cnc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 15, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 9, 9, 9, 9, 9, 9, 15, 15, 33, 33, 33, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 101 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534458094 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094 Building ZINC000534458094 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534458094 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 654) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/654: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cn1cnc2ccccc21) `ZINC000534458094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534458094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000534458094 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cn1cnc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 17, 32, 32, 32, 32, 32, 32, 32, 32, 3, 3, 3, 8, 8, 4, 8, 8, 3, 3, 3, 9, 9, 9, 9, 9, 9, 17, 17, 32, 32, 32, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 105 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 655) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/655: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cn1cnc2ccccc21) `ZINC000534458094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534458094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000534458094 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cn1cnc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 15, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 9, 9, 9, 9, 9, 9, 15, 15, 33, 33, 33, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 101 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534458094 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534458094 Building ZINC000508831022 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000508831022 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/656 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(n2cccn2)c(F)c1) `ZINC000508831022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000508831022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000508831022 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(n2cccn2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 27, 27, 27, 27, 35, 35, 35, 35, 27, 27, 27, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 4, 6, 6, 6, 27, 27, 35, 35, 35, 27] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 81 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/657 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(n2cccn2)c(F)c1) `ZINC000508831022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000508831022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000508831022 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(n2cccn2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 24, 24, 24, 24, 34, 34, 34, 34, 24, 24, 24, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 3, 6, 6, 6, 24, 24, 34, 34, 34, 24] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 88 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000508831022 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022 Building ZINC000508831022 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000508831022 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 656) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/656: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(n2cccn2)c(F)c1) `ZINC000508831022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000508831022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000508831022 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(n2cccn2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 27, 27, 27, 27, 35, 35, 35, 35, 27, 27, 27, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 4, 6, 6, 6, 27, 27, 35, 35, 35, 27] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 81 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 657) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/657: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(n2cccn2)c(F)c1) `ZINC000508831022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000508831022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000508831022 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(n2cccn2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 24, 24, 24, 24, 34, 34, 34, 34, 24, 24, 24, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 3, 6, 6, 6, 24, 24, 34, 34, 34, 24] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 88 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000508831022 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508831022 Building ZINC000534607926 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534607926 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/658 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccc(OCc2cccs2)c(OC)c1)C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000534607926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534607926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000534607926 none CCN(Cc1ccc(OCc2cccs2)c(OC)c1)C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 14, 1, 12, 5, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 3, 9, 19, 41, 41, 41, 41, 3, 3, 6, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 41, 41, 41, 6, 6, 6, 3, 2, 4, 4, 4, 4, 4, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 35, 32, 34, 19, 20, 21, 22, 23, 36, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/659 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccc(OCc2cccs2)c(OC)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000534607926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534607926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000534607926 none CCN(Cc1ccc(OCc2cccs2)c(OC)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 14, 1, 12, 5, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 3, 10, 21, 42, 42, 42, 42, 3, 3, 6, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 21, 21, 42, 42, 42, 6, 6, 6, 3, 2, 4, 4, 4, 4, 4, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 35, 32, 34, 19, 20, 21, 22, 23, 36, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534607926 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926 Building ZINC000534607926 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534607926 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 658) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/658: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccc(OCc2cccs2)c(OC)c1)C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000534607926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534607926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000534607926 none CCN(Cc1ccc(OCc2cccs2)c(OC)c1)C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 14, 1, 12, 5, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 3, 9, 19, 41, 41, 41, 41, 3, 3, 6, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 41, 41, 41, 6, 6, 6, 3, 2, 4, 4, 4, 4, 4, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 35, 32, 34, 19, 20, 21, 22, 23, 36, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 659) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/659: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccc(OCc2cccs2)c(OC)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000534607926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534607926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000534607926 none CCN(Cc1ccc(OCc2cccs2)c(OC)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 14, 1, 12, 5, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 3, 10, 21, 42, 42, 42, 42, 3, 3, 6, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 21, 21, 42, 42, 42, 6, 6, 6, 3, 2, 4, 4, 4, 4, 4, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 35, 32, 34, 19, 20, 21, 22, 23, 36, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534607926 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534607926 Building ZINC000534614046 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534614046 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/660 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(NC(=O)c3cccc(C(F)(F)F)c3)c2)cn1) `ZINC000534614046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534614046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000534614046 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(NC(=O)c3cccc(C(F)(F)F)c3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 8, 8, 8, 8, 8, 4, 2, 4, 4, 4, 8, 30, 30, 30, 30, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/661 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/661' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(NC(=O)c3cccc(C(F)(F)F)c3)c2)cn1) `ZINC000534614046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534614046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000534614046 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(NC(=O)c3cccc(C(F)(F)F)c3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 8, 8, 8, 32, 32, 8, 32, 32, 32, 32, 32, 32, 4, 5, 5, 9, 9, 9, 9, 9, 5, 2, 4, 4, 4, 8, 32, 32, 16, 32, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534614046 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046 Building ZINC000534614046 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534614046 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 660) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/660: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(NC(=O)c3cccc(C(F)(F)F)c3)c2)cn1) `ZINC000534614046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534614046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000534614046 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(NC(=O)c3cccc(C(F)(F)F)c3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 8, 8, 8, 8, 8, 4, 2, 4, 4, 4, 8, 30, 30, 30, 30, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 661) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/661: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(NC(=O)c3cccc(C(F)(F)F)c3)c2)cn1) `ZINC000534614046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534614046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000534614046 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(NC(=O)c3cccc(C(F)(F)F)c3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 8, 8, 8, 32, 32, 8, 32, 32, 32, 32, 32, 32, 4, 5, 5, 9, 9, 9, 9, 9, 5, 2, 4, 4, 4, 8, 32, 32, 16, 32, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534614046 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534614046 Building ZINC000534613890 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534613890 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/662 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCc3ccc4ccccc4n3)c2)cn1) `ZINC000534613890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534613890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000534613890 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCc3ccc4ccccc4n3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 13, 7, 7, 22, 30, 33, 33, 33, 33, 33, 33, 33, 33, 33, 7, 2, 2, 4, 4, 4, 4, 4, 2, 2, 7, 7, 13, 13, 13, 30, 30, 33, 33, 33, 33, 33, 33, 7, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/663 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/663' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCc3ccc4ccccc4n3)c2)cn1) `ZINC000534613890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534613890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000534613890 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCc3ccc4ccccc4n3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 16, 8, 8, 29, 41, 45, 45, 45, 45, 45, 45, 45, 45, 45, 8, 2, 2, 4, 4, 4, 4, 4, 2, 2, 8, 8, 16, 16, 16, 41, 41, 45, 45, 45, 45, 45, 45, 8, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534613890 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890 Building ZINC000534613890 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534613890 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 662) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/662: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCc3ccc4ccccc4n3)c2)cn1) `ZINC000534613890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534613890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000534613890 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCc3ccc4ccccc4n3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 13, 7, 7, 22, 30, 33, 33, 33, 33, 33, 33, 33, 33, 33, 7, 2, 2, 4, 4, 4, 4, 4, 2, 2, 7, 7, 13, 13, 13, 30, 30, 33, 33, 33, 33, 33, 33, 7, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 663) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/663: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCc3ccc4ccccc4n3)c2)cn1) `ZINC000534613890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534613890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000534613890 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCc3ccc4ccccc4n3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 16, 8, 8, 29, 41, 45, 45, 45, 45, 45, 45, 45, 45, 45, 8, 2, 2, 4, 4, 4, 4, 4, 2, 2, 8, 8, 16, 16, 16, 41, 41, 45, 45, 45, 45, 45, 45, 8, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534613890 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534613890 Building ZINC000534623498 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534623498 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/664 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2nc(C)c(Cc3cccc(Br)c3)s2)cn1) `ZINC000534623498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534623498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000534623498 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2nc(C)c(Cc3cccc(Br)c3)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 1, 5, 1, 1, 1, 1, 1, 17, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 12, 26, 26, 26, 26, 26, 26, 4, 2, 2, 5, 5, 5, 5, 5, 2, 2, 4, 4, 4, 12, 12, 26, 26, 26, 26, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 87 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/665 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/665' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2nc(C)c(Cc3cccc(Br)c3)s2)cn1) `ZINC000534623498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534623498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000534623498 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2nc(C)c(Cc3cccc(Br)c3)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 1, 5, 1, 1, 1, 1, 1, 17, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 12, 25, 25, 25, 25, 25, 25, 4, 3, 3, 7, 7, 7, 7, 7, 3, 2, 4, 4, 4, 12, 12, 25, 25, 25, 25, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534623498 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498 Building ZINC000534623498 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534623498 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 664) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/664: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2nc(C)c(Cc3cccc(Br)c3)s2)cn1) `ZINC000534623498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534623498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000534623498 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2nc(C)c(Cc3cccc(Br)c3)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 1, 5, 1, 1, 1, 1, 1, 17, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 12, 26, 26, 26, 26, 26, 26, 4, 2, 2, 5, 5, 5, 5, 5, 2, 2, 4, 4, 4, 12, 12, 26, 26, 26, 26, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 87 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 665) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/665: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2nc(C)c(Cc3cccc(Br)c3)s2)cn1) `ZINC000534623498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534623498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000534623498 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2nc(C)c(Cc3cccc(Br)c3)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 1, 5, 1, 1, 1, 1, 1, 17, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 12, 25, 25, 25, 25, 25, 25, 4, 3, 3, 7, 7, 7, 7, 7, 3, 2, 4, 4, 4, 12, 12, 25, 25, 25, 25, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534623498 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534623498 Building ZINC000534635160 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000534635160 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/666 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534635160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635160 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 11, 11, 10, 10, 11, 11, 13, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 10, 10, 10, 10, 10, 5, 2, 6, 6, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 107 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/667 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/667' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534635160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635160 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 13, 13, 12, 12, 13, 13, 15, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 14, 14, 14, 14, 14, 6, 2, 7, 7, 13, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/668 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/668' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635160.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000534635160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635160 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 11, 11, 10, 10, 11, 11, 13, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 10, 10, 10, 10, 10, 5, 2, 6, 6, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 107 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/669 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/669' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635160.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000534635160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635160 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 13, 13, 12, 12, 13, 13, 15, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 14, 14, 14, 14, 14, 6, 2, 7, 7, 13, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534635160 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 Building ZINC000534635160 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000534635160 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 666) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534635160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635160 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 11, 11, 10, 10, 11, 11, 13, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 10, 10, 10, 10, 10, 5, 2, 6, 6, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 107 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 667) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534635160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635160 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 13, 13, 12, 12, 13, 13, 15, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 14, 14, 14, 14, 14, 6, 2, 7, 7, 13, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 668) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635160.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000534635160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635160 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 11, 11, 10, 10, 11, 11, 13, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 10, 10, 10, 10, 10, 5, 2, 6, 6, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 107 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 669) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635160.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000534635160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635160 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 13, 13, 12, 12, 13, 13, 15, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 14, 14, 14, 14, 14, 6, 2, 7, 7, 13, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534635160 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 Building ZINC000534635160 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000534635160 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 666) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534635160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635160 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 11, 11, 10, 10, 11, 11, 13, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 10, 10, 10, 10, 10, 5, 2, 6, 6, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 107 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 667) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534635160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635160 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 13, 13, 12, 12, 13, 13, 15, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 14, 14, 14, 14, 14, 6, 2, 7, 7, 13, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 668) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635160.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000534635160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635160 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 11, 11, 10, 10, 11, 11, 13, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 10, 10, 10, 10, 10, 5, 2, 6, 6, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 107 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 669) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635160.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000534635160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635160 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 13, 13, 12, 12, 13, 13, 15, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 14, 14, 14, 14, 14, 6, 2, 7, 7, 13, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534635160 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 Building ZINC000534635160 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000534635160 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 666) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534635160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635160 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 11, 11, 10, 10, 11, 11, 13, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 10, 10, 10, 10, 10, 5, 2, 6, 6, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 107 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 667) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534635160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635160 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 13, 13, 12, 12, 13, 13, 15, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 14, 14, 14, 14, 14, 6, 2, 7, 7, 13, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 668) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635160.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000534635160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635160 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 11, 11, 10, 10, 11, 11, 13, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 10, 10, 10, 10, 10, 5, 2, 6, 6, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 107 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 669) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635160.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000534635160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635160 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 13, 13, 12, 12, 13, 13, 15, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 14, 14, 14, 14, 14, 6, 2, 7, 7, 13, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534635160 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635160 Building ZINC000534635161 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000534635161 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/670 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534635161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635161 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 13, 13, 12, 12, 13, 13, 15, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 14, 14, 14, 14, 14, 6, 2, 7, 7, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/671 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/671' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534635161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635161 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 11, 11, 10, 11, 11, 11, 13, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 10, 10, 10, 10, 10, 5, 2, 6, 6, 11, 11, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 111 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/672 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/672' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635161.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000534635161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635161 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 13, 13, 12, 12, 13, 13, 15, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 14, 14, 14, 14, 14, 6, 2, 7, 7, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/673 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/673' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635161.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000534635161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635161 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 11, 11, 10, 11, 11, 11, 13, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 10, 10, 10, 10, 10, 5, 2, 6, 6, 11, 11, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 111 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534635161 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 Building ZINC000534635161 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000534635161 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 670) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534635161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635161 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 13, 13, 12, 12, 13, 13, 15, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 14, 14, 14, 14, 14, 6, 2, 7, 7, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 671) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534635161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635161 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 11, 11, 10, 11, 11, 11, 13, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 10, 10, 10, 10, 10, 5, 2, 6, 6, 11, 11, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 111 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 672) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635161.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000534635161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635161 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 13, 13, 12, 12, 13, 13, 15, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 14, 14, 14, 14, 14, 6, 2, 7, 7, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 673) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635161.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000534635161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635161 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 11, 11, 10, 11, 11, 11, 13, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 10, 10, 10, 10, 10, 5, 2, 6, 6, 11, 11, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 111 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534635161 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 Building ZINC000534635161 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000534635161 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 670) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534635161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635161 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 13, 13, 12, 12, 13, 13, 15, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 14, 14, 14, 14, 14, 6, 2, 7, 7, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 671) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534635161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635161 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 11, 11, 10, 11, 11, 11, 13, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 10, 10, 10, 10, 10, 5, 2, 6, 6, 11, 11, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 111 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 672) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635161.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000534635161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635161 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 13, 13, 12, 12, 13, 13, 15, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 14, 14, 14, 14, 14, 6, 2, 7, 7, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 673) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635161.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000534635161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635161 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 11, 11, 10, 11, 11, 11, 13, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 10, 10, 10, 10, 10, 5, 2, 6, 6, 11, 11, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 111 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534635161 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 Building ZINC000534635161 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000534635161 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 670) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534635161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635161 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 13, 13, 12, 12, 13, 13, 15, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 14, 14, 14, 14, 14, 6, 2, 7, 7, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 671) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534635161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635161 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 11, 11, 10, 11, 11, 11, 13, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 10, 10, 10, 10, 10, 5, 2, 6, 6, 11, 11, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 111 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 672) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635161.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000534635161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635161 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 13, 13, 12, 12, 13, 13, 15, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 14, 14, 14, 14, 14, 6, 2, 7, 7, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 673) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1) `ZINC000534635161.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000534635161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534635161 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 11, 11, 10, 11, 11, 11, 13, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 10, 10, 10, 10, 10, 5, 2, 6, 6, 11, 11, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 111 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534635161 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534635161 Building ZINC000534668040 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534668040 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/674 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(Cl)cc3)cc2C(=O)OC)cn1) `ZINC000534668040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534668040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000534668040 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(Cl)cc3)cc2C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 23, 24, 24, 24, 24, 24, 24, 4, 4, 4, 6, 6, 6, 4, 4, 5, 5, 5, 5, 5, 4, 2, 4, 4, 24, 24, 24, 24, 4, 6, 6, 6, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/675 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(Cl)cc3)cc2C(=O)OC)cn1) `ZINC000534668040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534668040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000534668040 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(Cl)cc3)cc2C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 21, 22, 22, 21, 22, 22, 22, 4, 4, 4, 7, 7, 7, 5, 5, 7, 7, 7, 7, 7, 5, 2, 4, 4, 22, 22, 22, 22, 4, 7, 7, 7, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534668040 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040 Building ZINC000534668040 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534668040 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 674) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/674: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(Cl)cc3)cc2C(=O)OC)cn1) `ZINC000534668040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534668040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000534668040 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(Cl)cc3)cc2C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 23, 24, 24, 24, 24, 24, 24, 4, 4, 4, 6, 6, 6, 4, 4, 5, 5, 5, 5, 5, 4, 2, 4, 4, 24, 24, 24, 24, 4, 6, 6, 6, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 675) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/675: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(Cl)cc3)cc2C(=O)OC)cn1) `ZINC000534668040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534668040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000534668040 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(Cl)cc3)cc2C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 21, 22, 22, 21, 22, 22, 22, 4, 4, 4, 7, 7, 7, 5, 5, 7, 7, 7, 7, 7, 5, 2, 4, 4, 22, 22, 22, 22, 4, 7, 7, 7, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534668040 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534668040 Building ZINC000534661725 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534661725 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/676 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCCO)Cc1ccc(Cl)c(Cl)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000534661725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534661725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000534661725 none O=C(N(CCCO)Cc1ccc(Cl)c(Cl)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 6, 10, 1, 2, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 9, 10, 30, 2, 2, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 7, 16, 17, 18] set([4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/677 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/677' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCCO)Cc1ccc(Cl)c(Cl)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000534661725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534661725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000534661725 none O=C(N(CCCO)Cc1ccc(Cl)c(Cl)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 6, 10, 1, 2, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 10, 9, 30, 2, 2, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 7, 16, 17, 18] set([4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534661725 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725 Building ZINC000534661725 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534661725 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 676) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/676: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCCO)Cc1ccc(Cl)c(Cl)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000534661725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534661725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000534661725 none O=C(N(CCCO)Cc1ccc(Cl)c(Cl)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 6, 10, 1, 2, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 9, 10, 30, 2, 2, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 7, 16, 17, 18] set([4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 677) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/677: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCCO)Cc1ccc(Cl)c(Cl)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000534661725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534661725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000534661725 none O=C(N(CCCO)Cc1ccc(Cl)c(Cl)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 6, 10, 1, 2, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 10, 9, 30, 2, 2, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 7, 16, 17, 18] set([4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534661725 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534661725 Building ZINC000534689580 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534689580 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/678 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Br)cc2Oc2ccccc2)cn1) `ZINC000534689580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534689580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000534689580 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Br)cc2Oc2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 14, 19, 19, 19, 19, 19, 19, 19, 22, 22, 22, 22, 22, 22, 4, 4, 7, 7, 7, 7, 7, 4, 2, 14, 14, 19, 19, 19, 22, 22, 22, 22, 22, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/679 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Br)cc2Oc2ccccc2)cn1) `ZINC000534689580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534689580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000534689580 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Br)cc2Oc2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 14, 19, 19, 17, 19, 19, 19, 19, 22, 22, 22, 22, 22, 22, 4, 4, 7, 7, 7, 7, 7, 4, 2, 14, 14, 19, 19, 19, 22, 22, 22, 22, 22, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534689580 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580 Building ZINC000534689580 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534689580 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 678) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/678: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Br)cc2Oc2ccccc2)cn1) `ZINC000534689580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534689580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000534689580 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Br)cc2Oc2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 14, 19, 19, 19, 19, 19, 19, 19, 22, 22, 22, 22, 22, 22, 4, 4, 7, 7, 7, 7, 7, 4, 2, 14, 14, 19, 19, 19, 22, 22, 22, 22, 22, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 679) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/679: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Br)cc2Oc2ccccc2)cn1) `ZINC000534689580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534689580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000534689580 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Br)cc2Oc2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 14, 19, 19, 17, 19, 19, 19, 19, 22, 22, 22, 22, 22, 22, 4, 4, 7, 7, 7, 7, 7, 4, 2, 14, 14, 19, 19, 19, 22, 22, 22, 22, 22, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534689580 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534689580 Building ZINC000534695712 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534695712 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/680 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(NC(=O)c4ccc(C)s4)sc3c2)cn1) `ZINC000534695712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534695712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000534695712 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(NC(=O)c4ccc(C)s4)sc3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 14, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 19, 19, 19, 22, 22, 22, 22, 22, 10, 10, 10, 6, 6, 12, 12, 12, 12, 12, 6, 2, 10, 10, 19, 22, 22, 22, 22, 22, 10, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/681 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(NC(=O)c4ccc(C)s4)sc3c2)cn1) `ZINC000534695712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534695712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000534695712 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(NC(=O)c4ccc(C)s4)sc3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 14, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 17, 17, 17, 25, 25, 25, 25, 25, 9, 9, 9, 6, 6, 9, 9, 9, 9, 9, 6, 2, 9, 9, 17, 25, 25, 25, 25, 25, 9, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534695712 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712 Building ZINC000534695712 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534695712 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 680) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(NC(=O)c4ccc(C)s4)sc3c2)cn1) `ZINC000534695712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534695712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000534695712 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(NC(=O)c4ccc(C)s4)sc3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 14, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 19, 19, 19, 22, 22, 22, 22, 22, 10, 10, 10, 6, 6, 12, 12, 12, 12, 12, 6, 2, 10, 10, 19, 22, 22, 22, 22, 22, 10, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 681) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(NC(=O)c4ccc(C)s4)sc3c2)cn1) `ZINC000534695712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534695712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000534695712 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(NC(=O)c4ccc(C)s4)sc3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 14, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 17, 17, 17, 25, 25, 25, 25, 25, 9, 9, 9, 6, 6, 9, 9, 9, 9, 9, 6, 2, 9, 9, 17, 25, 25, 25, 25, 25, 9, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534695712 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534695712 Building ZINC000429774977 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429774977 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/682 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429774977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429774977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000429774977 none C[C@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 14, 8, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 12, 12, 25, 25, 25, 43, 43, 43, 43, 25, 25, 5, 5, 5, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 12, 12, 12, 43, 43, 43, 5, 5, 5, 5, 2, 2, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/683 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429774977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429774977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000429774977 none C[C@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 14, 8, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 14, 14, 27, 27, 27, 47, 47, 47, 47, 27, 27, 7, 7, 7, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 14, 14, 14, 47, 47, 47, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 99 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000429774977 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977 Building ZINC000429774977 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429774977 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 682) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/682: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429774977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429774977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000429774977 none C[C@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 14, 8, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 12, 12, 25, 25, 25, 43, 43, 43, 43, 25, 25, 5, 5, 5, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 12, 12, 12, 43, 43, 43, 5, 5, 5, 5, 2, 2, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 683) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/683: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429774977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429774977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000429774977 none C[C@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 14, 8, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 14, 14, 27, 27, 27, 47, 47, 47, 47, 27, 27, 7, 7, 7, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 14, 14, 14, 47, 47, 47, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 99 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000429774977 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774977 Building ZINC000429774978 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429774978 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/684 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429774978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429774978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000429774978 none C[C@@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 14, 8, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 11, 28, 28, 28, 43, 43, 43, 43, 28, 28, 3, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 43, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/685 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/685' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429774978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429774978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000429774978 none C[C@@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 14, 8, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 16, 16, 24, 24, 24, 43, 43, 43, 43, 24, 24, 5, 5, 5, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 16, 16, 16, 43, 43, 43, 5, 5, 5, 5, 2, 2, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000429774978 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978 Building ZINC000429774978 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429774978 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 684) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/684: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429774978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429774978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000429774978 none C[C@@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 14, 8, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 11, 28, 28, 28, 43, 43, 43, 43, 28, 28, 3, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 43, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 685) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/685: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000429774978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429774978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000429774978 none C[C@@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 14, 8, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 16, 16, 24, 24, 24, 43, 43, 43, 43, 24, 24, 5, 5, 5, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 16, 16, 16, 43, 43, 43, 5, 5, 5, 5, 2, 2, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000429774978 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000429774978 Building ZINC000534736682 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534736682 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/686 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3ccccc3OC)nn2c2ccc(C)cc2)cn1) `ZINC000534736682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534736682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000534736682 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3ccccc3OC)nn2c2ccc(C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 29, 29, 13, 29, 29, 29, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 11, 11, 11, 11, 11, 5, 2, 4, 29, 29, 29, 29, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/687 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(c3ccccc3OC)nn2c2ccc(C)cc2)cn1) `ZINC000534736682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534736682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000534736682 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(c3ccccc3OC)nn2c2ccc(C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 30, 30, 11, 30, 30, 30, 33, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 12, 12, 12, 12, 12, 5, 2, 4, 30, 30, 30, 30, 33, 33, 33, 4, 4, 4, 4, 4, 4, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534736682 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682 Building ZINC000534736682 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534736682 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 686) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/686: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3ccccc3OC)nn2c2ccc(C)cc2)cn1) `ZINC000534736682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534736682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000534736682 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3ccccc3OC)nn2c2ccc(C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 29, 29, 13, 29, 29, 29, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 11, 11, 11, 11, 11, 5, 2, 4, 29, 29, 29, 29, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 687) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/687: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(c3ccccc3OC)nn2c2ccc(C)cc2)cn1) `ZINC000534736682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534736682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000534736682 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(c3ccccc3OC)nn2c2ccc(C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 30, 30, 11, 30, 30, 30, 33, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 12, 12, 12, 12, 12, 5, 2, 4, 30, 30, 30, 30, 33, 33, 33, 4, 4, 4, 4, 4, 4, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534736682 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534736682 Building ZINC000534735796 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534735796 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/688 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3cccc(OC)c3)nn2c2ccc(C)cc2)cn1) `ZINC000534735796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534735796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000534735796 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3cccc(OC)c3)nn2c2ccc(C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 25, 25, 25, 25, 25, 27, 25, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 11, 11, 11, 11, 11, 5, 2, 4, 25, 25, 25, 27, 27, 27, 25, 4, 4, 4, 4, 4, 4, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/689 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/689' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(c3cccc(OC)c3)nn2c2ccc(C)cc2)cn1) `ZINC000534735796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534735796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000534735796 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(c3cccc(OC)c3)nn2c2ccc(C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 25, 25, 25, 25, 25, 28, 25, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 11, 11, 11, 11, 11, 5, 2, 4, 25, 25, 25, 28, 28, 28, 25, 4, 4, 4, 4, 4, 4, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534735796 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796 Building ZINC000534735796 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534735796 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 688) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/688: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3cccc(OC)c3)nn2c2ccc(C)cc2)cn1) `ZINC000534735796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534735796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000534735796 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3cccc(OC)c3)nn2c2ccc(C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 25, 25, 25, 25, 25, 27, 25, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 11, 11, 11, 11, 11, 5, 2, 4, 25, 25, 25, 27, 27, 27, 25, 4, 4, 4, 4, 4, 4, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 689) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/689: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(c3cccc(OC)c3)nn2c2ccc(C)cc2)cn1) `ZINC000534735796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534735796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000534735796 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(c3cccc(OC)c3)nn2c2ccc(C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 25, 25, 25, 25, 25, 28, 25, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 11, 11, 11, 11, 11, 5, 2, 4, 25, 25, 25, 28, 28, 28, 25, 4, 4, 4, 4, 4, 4, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534735796 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534735796 Building ZINC000534737546 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534737546 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/690 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2c(c3ccc(Cl)cc3)c(C(F)(F)F)nn2C)cn1) `ZINC000534737546.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534737546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000534737546 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2c(c3ccc(Cl)cc3)c(C(F)(F)F)nn2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 5, 15, 15, 15, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 7, 7, 1, 1, 1, 1, 4, 4, 8, 17, 17, 26, 26, 20, 24, 26, 26, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 15, 15, 15, 15, 15, 7, 8, 26, 26, 26, 26, 17, 17, 17, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/691 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2c(c3ccc(Cl)cc3)c(C(F)(F)F)nn2C)cn1) `ZINC000534737546.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534737546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000534737546 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2c(c3ccc(Cl)cc3)c(C(F)(F)F)nn2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 5, 15, 15, 15, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 7, 7, 1, 1, 1, 1, 4, 4, 8, 15, 15, 25, 25, 20, 20, 25, 25, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 15, 15, 15, 15, 15, 7, 8, 25, 25, 25, 25, 15, 15, 15, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534737546 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546 Building ZINC000534737546 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534737546 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 690) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/690: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2c(c3ccc(Cl)cc3)c(C(F)(F)F)nn2C)cn1) `ZINC000534737546.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534737546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000534737546 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2c(c3ccc(Cl)cc3)c(C(F)(F)F)nn2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 5, 15, 15, 15, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 7, 7, 1, 1, 1, 1, 4, 4, 8, 17, 17, 26, 26, 20, 24, 26, 26, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 15, 15, 15, 15, 15, 7, 8, 26, 26, 26, 26, 17, 17, 17, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 691) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/691: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2c(c3ccc(Cl)cc3)c(C(F)(F)F)nn2C)cn1) `ZINC000534737546.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534737546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000534737546 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2c(c3ccc(Cl)cc3)c(C(F)(F)F)nn2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 5, 15, 15, 15, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 7, 7, 1, 1, 1, 1, 4, 4, 8, 15, 15, 25, 25, 20, 20, 25, 25, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 15, 15, 15, 15, 15, 7, 8, 25, 25, 25, 25, 15, 15, 15, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534737546 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534737546 Building ZINC000534776992 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534776992 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/692 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(F)cc2c2nc(CCOc3ccccc3)no2)cn1) `ZINC000534776992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534776992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534776992 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(F)cc2c2nc(CCOc3ccccc3)no2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 15, 15, 33, 34, 34, 33, 34, 34, 9, 9, 6, 6, 11, 11, 11, 11, 11, 6, 2, 4, 4, 4, 15, 15, 15, 15, 34, 34, 33, 34, 34, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/693 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(F)cc2c2nc(CCOc3ccccc3)no2)cn1) `ZINC000534776992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534776992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534776992 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(F)cc2c2nc(CCOc3ccccc3)no2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 16, 16, 32, 33, 33, 32, 33, 33, 10, 10, 6, 6, 12, 12, 12, 12, 12, 6, 3, 5, 5, 5, 16, 16, 16, 16, 33, 33, 32, 33, 33, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534776992 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992 Building ZINC000534776992 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534776992 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 692) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/692: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(F)cc2c2nc(CCOc3ccccc3)no2)cn1) `ZINC000534776992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534776992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534776992 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(F)cc2c2nc(CCOc3ccccc3)no2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 15, 15, 33, 34, 34, 33, 34, 34, 9, 9, 6, 6, 11, 11, 11, 11, 11, 6, 2, 4, 4, 4, 15, 15, 15, 15, 34, 34, 33, 34, 34, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 693) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/693: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(F)cc2c2nc(CCOc3ccccc3)no2)cn1) `ZINC000534776992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534776992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000534776992 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(F)cc2c2nc(CCOc3ccccc3)no2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 16, 16, 32, 33, 33, 32, 33, 33, 10, 10, 6, 6, 12, 12, 12, 12, 12, 6, 3, 5, 5, 5, 16, 16, 16, 16, 33, 33, 32, 33, 33, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534776992 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534776992 Building ZINC000534803533 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534803533 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/694 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)nc2ccccc21) `ZINC000534803533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534803533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000534803533 none CCNC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)nc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 21, 21, 4, 21, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 21, 4, 2, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 127 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/695 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)nc2ccccc21) `ZINC000534803533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534803533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000534803533 none CCNC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)nc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 17, 17, 4, 17, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 17, 4, 2, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534803533 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533 Building ZINC000534803533 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534803533 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 694) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/694: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)nc2ccccc21) `ZINC000534803533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534803533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000534803533 none CCNC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)nc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 21, 21, 4, 21, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 21, 4, 2, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 127 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 695) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/695: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)nc2ccccc21) `ZINC000534803533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534803533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000534803533 none CCNC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)nc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 17, 17, 4, 17, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 17, 4, 2, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534803533 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534803533 Building ZINC000534831472 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534831472 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/696 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1nc(c2ccccc2)no1) `ZINC000534831472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534831472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000534831472 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1nc(c2ccccc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 11, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 7, 7, 11, 11, 11, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/697 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1nc(c2ccccc2)no1) `ZINC000534831472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534831472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000534831472 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1nc(c2ccccc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 6, 6, 10, 10, 10, 50, 50, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534831472 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472 Building ZINC000534831472 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534831472 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 696) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/696: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1nc(c2ccccc2)no1) `ZINC000534831472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534831472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000534831472 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1nc(c2ccccc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 11, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 7, 7, 11, 11, 11, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 697) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/697: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1nc(c2ccccc2)no1) `ZINC000534831472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534831472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000534831472 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1nc(c2ccccc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 6, 6, 10, 10, 10, 50, 50, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534831472 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831472 Building ZINC000534831475 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534831475 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/698 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1nc(c2ccccc2)no1) `ZINC000534831475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534831475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000534831475 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1nc(c2ccccc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 6, 6, 10, 10, 10, 50, 50, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/699 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1nc(c2ccccc2)no1) `ZINC000534831475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534831475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000534831475 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1nc(c2ccccc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 11, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 7, 7, 11, 11, 11, 48, 48, 48, 48, 48] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534831475 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475 Building ZINC000534831475 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534831475 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 698) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1nc(c2ccccc2)no1) `ZINC000534831475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534831475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000534831475 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1nc(c2ccccc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 6, 6, 10, 10, 10, 50, 50, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 699) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1nc(c2ccccc2)no1) `ZINC000534831475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534831475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000534831475 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1nc(c2ccccc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 11, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 7, 7, 11, 11, 11, 48, 48, 48, 48, 48] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534831475 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534831475 Building ZINC000534843787 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534843787 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/700 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccn1) `ZINC000534843787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534843787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000534843787 none COc1ccccc1[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 13, 13, 13, 6, 13, 13, 3, 2, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 3, 18, 18, 18, 18, 18, 21, 21, 21, 13, 13, 13, 13, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 18, 18, 18, 18] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 97 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/701 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccn1) `ZINC000534843787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534843787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000534843787 none COc1ccccc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 10, 10, 5, 10, 10, 3, 2, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 3, 15, 15, 15, 15, 15, 18, 18, 18, 10, 10, 10, 10, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534843787 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787 Building ZINC000534843787 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534843787 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 700) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/700: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccn1) `ZINC000534843787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534843787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000534843787 none COc1ccccc1[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 13, 13, 13, 6, 13, 13, 3, 2, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 3, 18, 18, 18, 18, 18, 21, 21, 21, 13, 13, 13, 13, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 18, 18, 18, 18] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 97 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 701) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/701: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccn1) `ZINC000534843787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534843787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000534843787 none COc1ccccc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 10, 10, 5, 10, 10, 3, 2, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 3, 15, 15, 15, 15, 15, 18, 18, 18, 10, 10, 10, 10, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534843787 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843787 Building ZINC000534843788 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534843788 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/702 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccn1) `ZINC000534843788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534843788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000534843788 none COc1ccccc1[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 10, 10, 6, 10, 10, 6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 6, 13, 13, 13, 13, 13, 14, 14, 14, 10, 10, 10, 10, 3, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 13, 13, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/703 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/703' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccn1) `ZINC000534843788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534843788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000534843788 none COc1ccccc1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 12, 12, 12, 7, 12, 12, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12, 2, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 4, 19, 19, 19, 19] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 109 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534843788 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788 Building ZINC000534843788 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534843788 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 702) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccn1) `ZINC000534843788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534843788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000534843788 none COc1ccccc1[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 10, 10, 6, 10, 10, 6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 6, 13, 13, 13, 13, 13, 14, 14, 14, 10, 10, 10, 10, 3, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 13, 13, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 703) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccn1) `ZINC000534843788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534843788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000534843788 none COc1ccccc1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 12, 12, 12, 7, 12, 12, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12, 2, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 4, 19, 19, 19, 19] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 109 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000534843788 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000534843788 Building ZINC000546873771 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546873771 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/704 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2cc(Br)ccc2OC)cc1Cl) `ZINC000546873771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546873771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546873771 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2cc(Br)ccc2OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 5, 5, 9, 15, 15, 15, 15, 15, 15, 15, 23, 4, 4, 4, 8, 8, 8, 4, 4, 5, 5, 5, 9, 9, 15, 15, 15, 23, 23, 23, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/705 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/705' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2cc(Br)ccc2OC)cc1Cl) `ZINC000546873771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546873771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546873771 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2cc(Br)ccc2OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 5, 5, 9, 15, 15, 15, 13, 15, 15, 15, 23, 4, 4, 4, 8, 8, 8, 4, 4, 5, 5, 5, 9, 9, 15, 15, 15, 23, 23, 23, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000546873771 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771 Building ZINC000546873771 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546873771 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 704) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/704: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2cc(Br)ccc2OC)cc1Cl) `ZINC000546873771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546873771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546873771 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2cc(Br)ccc2OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 5, 5, 9, 15, 15, 15, 15, 15, 15, 15, 23, 4, 4, 4, 8, 8, 8, 4, 4, 5, 5, 5, 9, 9, 15, 15, 15, 23, 23, 23, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 705) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/705: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2cc(Br)ccc2OC)cc1Cl) `ZINC000546873771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546873771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546873771 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2cc(Br)ccc2OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 5, 5, 9, 15, 15, 15, 13, 15, 15, 15, 23, 4, 4, 4, 8, 8, 8, 4, 4, 5, 5, 5, 9, 9, 15, 15, 15, 23, 23, 23, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000546873771 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546873771 Building ZINC000535155661 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535155661 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/706 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1ccncc1C) `ZINC000535155661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535155661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000535155661 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1ccncc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 7, 12, 12, 12, 12, 12, 12, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 5, 5, 7, 7, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/707 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/707' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1ccncc1C) `ZINC000535155661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535155661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000535155661 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1ccncc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 8, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 6, 6, 8, 8, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535155661 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661 Building ZINC000535155661 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535155661 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 706) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1ccncc1C) `ZINC000535155661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535155661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000535155661 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1ccncc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 7, 12, 12, 12, 12, 12, 12, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 5, 5, 7, 7, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 707) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1ccncc1C) `ZINC000535155661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535155661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000535155661 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1ccncc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 8, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 6, 6, 8, 8, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535155661 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535155661 Building ZINC000535187586 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535187586 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/708 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCSc1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000535187586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535187586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000535187586 none COC(=O)CCSc1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 14, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 16, 39, 10, 10, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 7, 39, 39, 39, 16, 16, 10, 10, 7, 7, 7, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/709 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/709' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCSc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000535187586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535187586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000535187586 none COC(=O)CCSc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 14, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 16, 37, 10, 10, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 7, 37, 37, 37, 16, 16, 10, 10, 7, 7, 7, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535187586 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586 Building ZINC000535187586 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535187586 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 708) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCSc1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000535187586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535187586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000535187586 none COC(=O)CCSc1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 14, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 16, 39, 10, 10, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 7, 39, 39, 39, 16, 16, 10, 10, 7, 7, 7, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 709) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCSc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000535187586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535187586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000535187586 none COC(=O)CCSc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 14, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 16, 37, 10, 10, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 7, 37, 37, 37, 16, 16, 10, 10, 7, 7, 7, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535187586 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535187586 Building ZINC000535280700 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535280700 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/710 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCCO)Cc1cccc(Cl)c1) `ZINC000535280700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535280700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000535280700 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCCO)Cc1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 4, 10, 10, 14, 4, 10, 25, 25, 25, 25, 25, 24, 3, 3, 3, 8, 8, 4, 8, 8, 3, 3, 3, 10, 10, 10, 10, 14, 14, 42, 10, 10, 25, 25, 25, 25] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 179 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/711 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCCO)Cc1cccc(Cl)c1) `ZINC000535280700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535280700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000535280700 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCCO)Cc1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 4, 9, 9, 14, 4, 8, 23, 23, 23, 23, 23, 22, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 9, 9, 9, 9, 14, 14, 42, 8, 8, 23, 23, 23, 23] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 165 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535280700 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700 Building ZINC000535280700 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535280700 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 710) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCCO)Cc1cccc(Cl)c1) `ZINC000535280700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535280700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000535280700 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCCO)Cc1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 4, 10, 10, 14, 4, 10, 25, 25, 25, 25, 25, 24, 3, 3, 3, 8, 8, 4, 8, 8, 3, 3, 3, 10, 10, 10, 10, 14, 14, 42, 10, 10, 25, 25, 25, 25] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 179 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 711) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCCO)Cc1cccc(Cl)c1) `ZINC000535280700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535280700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000535280700 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCCO)Cc1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 4, 9, 9, 14, 4, 8, 23, 23, 23, 23, 23, 22, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 9, 9, 9, 9, 14, 14, 42, 8, 8, 23, 23, 23, 23] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 165 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535280700 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535280700 Building ZINC000535335661 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535335661 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/712 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2cccc(OC)c2OC)cn1) `ZINC000535335661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535335661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000535335661 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2cccc(OC)c2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 24, 24, 24, 24, 24, 28, 24, 24, 27, 5, 5, 7, 7, 7, 7, 7, 5, 2, 13, 13, 32, 32, 32, 32, 32, 24, 24, 24, 28, 28, 28, 27, 27, 27, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/713 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2cccc(OC)c2OC)cn1) `ZINC000535335661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535335661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000535335661 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2cccc(OC)c2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 21, 21, 30, 30, 30, 30, 30, 30, 30, 30, 30, 21, 23, 23, 23, 23, 23, 26, 23, 23, 27, 5, 5, 8, 8, 8, 8, 8, 5, 2, 14, 14, 30, 30, 30, 30, 30, 23, 23, 23, 26, 26, 26, 27, 27, 27, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535335661 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661 Building ZINC000535335661 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535335661 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 712) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/712: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2cccc(OC)c2OC)cn1) `ZINC000535335661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535335661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000535335661 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2cccc(OC)c2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 24, 24, 24, 24, 24, 28, 24, 24, 27, 5, 5, 7, 7, 7, 7, 7, 5, 2, 13, 13, 32, 32, 32, 32, 32, 24, 24, 24, 28, 28, 28, 27, 27, 27, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 713) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/713: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2cccc(OC)c2OC)cn1) `ZINC000535335661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535335661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000535335661 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2cccc(OC)c2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 21, 21, 30, 30, 30, 30, 30, 30, 30, 30, 30, 21, 23, 23, 23, 23, 23, 26, 23, 23, 27, 5, 5, 8, 8, 8, 8, 8, 5, 2, 14, 14, 30, 30, 30, 30, 30, 23, 23, 23, 26, 26, 26, 27, 27, 27, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535335661 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335661 Building ZINC000535335676 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535335676 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/714 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2cccc(OC)c2OC)cn1) `ZINC000535335676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535335676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000535335676 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2cccc(OC)c2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 22, 22, 32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 24, 24, 24, 24, 24, 27, 24, 24, 27, 5, 5, 8, 8, 8, 8, 8, 5, 2, 14, 14, 32, 32, 32, 32, 32, 24, 24, 24, 27, 27, 27, 27, 27, 27, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/715 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/715' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2cccc(OC)c2OC)cn1) `ZINC000535335676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535335676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000535335676 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2cccc(OC)c2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 20, 20, 33, 33, 33, 33, 33, 33, 33, 33, 33, 20, 22, 22, 22, 22, 22, 26, 22, 22, 25, 5, 5, 7, 7, 7, 7, 7, 5, 2, 13, 13, 33, 33, 33, 33, 33, 22, 22, 22, 26, 26, 26, 25, 25, 25, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535335676 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676 Building ZINC000535335676 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535335676 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 714) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2cccc(OC)c2OC)cn1) `ZINC000535335676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535335676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000535335676 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2cccc(OC)c2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 22, 22, 32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 24, 24, 24, 24, 24, 27, 24, 24, 27, 5, 5, 8, 8, 8, 8, 8, 5, 2, 14, 14, 32, 32, 32, 32, 32, 24, 24, 24, 27, 27, 27, 27, 27, 27, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 715) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2cccc(OC)c2OC)cn1) `ZINC000535335676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535335676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000535335676 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2cccc(OC)c2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 20, 20, 33, 33, 33, 33, 33, 33, 33, 33, 33, 20, 22, 22, 22, 22, 22, 26, 22, 22, 25, 5, 5, 7, 7, 7, 7, 7, 5, 2, 13, 13, 33, 33, 33, 33, 33, 22, 22, 22, 26, 26, 26, 25, 25, 25, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535335676 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535335676 Building ZINC000535375341 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535375341 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/716 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(CNC(=O)Nc3ccccc3Cl)c2)cn1) `ZINC000535375341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535375341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000535375341 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(CNC(=O)Nc3ccccc3Cl)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 2, 7, 7, 10, 23, 23, 23, 25, 40, 40, 25, 40, 40, 40, 7, 3, 3, 5, 5, 5, 5, 5, 3, 2, 7, 7, 4, 10, 10, 23, 25, 40, 40, 40, 40, 7, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/717 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/717' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(CNC(=O)Nc3ccccc3Cl)c2)cn1) `ZINC000535375341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535375341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000535375341 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(CNC(=O)Nc3ccccc3Cl)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 2, 7, 7, 9, 19, 19, 19, 21, 33, 33, 21, 33, 33, 33, 7, 3, 3, 5, 5, 5, 5, 5, 3, 2, 7, 7, 2, 9, 9, 19, 21, 33, 33, 33, 33, 7, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535375341 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341 Building ZINC000535375341 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535375341 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 716) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/716: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(CNC(=O)Nc3ccccc3Cl)c2)cn1) `ZINC000535375341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535375341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000535375341 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(CNC(=O)Nc3ccccc3Cl)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 2, 7, 7, 10, 23, 23, 23, 25, 40, 40, 25, 40, 40, 40, 7, 3, 3, 5, 5, 5, 5, 5, 3, 2, 7, 7, 4, 10, 10, 23, 25, 40, 40, 40, 40, 7, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 717) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/717: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(CNC(=O)Nc3ccccc3Cl)c2)cn1) `ZINC000535375341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535375341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000535375341 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(CNC(=O)Nc3ccccc3Cl)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 2, 7, 7, 9, 19, 19, 19, 21, 33, 33, 21, 33, 33, 33, 7, 3, 3, 5, 5, 5, 5, 5, 3, 2, 7, 7, 2, 9, 9, 19, 21, 33, 33, 33, 33, 7, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535375341 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535375341 Building ZINC000535388767 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535388767 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/718 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3c(cccc3NC(=O)Nc3ccc(C)cc3)C2)cn1) `ZINC000535388767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535388767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000535388767 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3c(cccc3NC(=O)Nc3ccc(C)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 18, 32, 32, 18, 18, 32, 32, 5, 3, 3, 5, 5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 17, 18, 32, 32, 32, 32, 32, 32, 32, 5, 5, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/719 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/719' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCc3c(cccc3NC(=O)Nc3ccc(C)cc3)C2)cn1) `ZINC000535388767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535388767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000535388767 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCc3c(cccc3NC(=O)Nc3ccc(C)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 18, 32, 32, 18, 18, 32, 32, 5, 3, 3, 5, 5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 17, 18, 32, 32, 32, 32, 32, 32, 32, 5, 5, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535388767 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767 Building ZINC000535388767 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535388767 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 718) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3c(cccc3NC(=O)Nc3ccc(C)cc3)C2)cn1) `ZINC000535388767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535388767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000535388767 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3c(cccc3NC(=O)Nc3ccc(C)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 18, 32, 32, 18, 18, 32, 32, 5, 3, 3, 5, 5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 17, 18, 32, 32, 32, 32, 32, 32, 32, 5, 5, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 719) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCc3c(cccc3NC(=O)Nc3ccc(C)cc3)C2)cn1) `ZINC000535388767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535388767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000535388767 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCc3c(cccc3NC(=O)Nc3ccc(C)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 18, 32, 32, 18, 18, 32, 32, 5, 3, 3, 5, 5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 17, 18, 32, 32, 32, 32, 32, 32, 32, 5, 5, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535388767 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535388767 Building ZINC000535396953 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535396953 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/720 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCc3c(NC(=O)Nc4ccccc4F)cccc32)cn1) `ZINC000535396953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535396953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000535396953 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCc3c(NC(=O)Nc4ccccc4F)cccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 14, 14, 15, 34, 34, 15, 34, 34, 34, 3, 3, 3, 3, 2, 2, 4, 4, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 13, 15, 34, 34, 34, 34, 3, 3, 3, 2] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/721 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/721' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCc3c(NC(=O)Nc4ccccc4F)cccc32)cn1) `ZINC000535396953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535396953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000535396953 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCc3c(NC(=O)Nc4ccccc4F)cccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 13, 13, 14, 33, 33, 19, 33, 33, 33, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 12, 14, 33, 33, 32, 33, 2, 2, 2, 2] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535396953 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953 Building ZINC000535396953 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535396953 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 720) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/720: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCc3c(NC(=O)Nc4ccccc4F)cccc32)cn1) `ZINC000535396953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535396953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000535396953 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCc3c(NC(=O)Nc4ccccc4F)cccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 14, 14, 15, 34, 34, 15, 34, 34, 34, 3, 3, 3, 3, 2, 2, 4, 4, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 13, 15, 34, 34, 34, 34, 3, 3, 3, 2] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 721) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/721: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCc3c(NC(=O)Nc4ccccc4F)cccc32)cn1) `ZINC000535396953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535396953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000535396953 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCc3c(NC(=O)Nc4ccccc4F)cccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 13, 13, 14, 33, 33, 19, 33, 33, 33, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 12, 14, 33, 33, 32, 33, 2, 2, 2, 2] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535396953 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535396953 Building ZINC000535393538 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535393538 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/722 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)c(NC(=O)c3ccncc3)c(Cl)c2)cn1) `ZINC000535393538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535393538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000535393538 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)c(NC(=O)c3ccncc3)c(Cl)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 19, 19, 19, 26, 26, 19, 26, 26, 4, 4, 4, 5, 5, 10, 10, 10, 10, 10, 5, 2, 4, 19, 26, 26, 26, 26, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/723 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/723' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)c(NC(=O)c3ccncc3)c(Cl)c2)cn1) `ZINC000535393538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535393538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000535393538 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)c(NC(=O)c3ccncc3)c(Cl)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 2, 4, 19, 19, 19, 25, 25, 19, 25, 25, 4, 4, 4, 5, 5, 10, 10, 10, 10, 10, 5, 2, 4, 19, 25, 25, 25, 25, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535393538 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538 Building ZINC000535393538 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535393538 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 722) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)c(NC(=O)c3ccncc3)c(Cl)c2)cn1) `ZINC000535393538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535393538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000535393538 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)c(NC(=O)c3ccncc3)c(Cl)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 19, 19, 19, 26, 26, 19, 26, 26, 4, 4, 4, 5, 5, 10, 10, 10, 10, 10, 5, 2, 4, 19, 26, 26, 26, 26, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 723) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)c(NC(=O)c3ccncc3)c(Cl)c2)cn1) `ZINC000535393538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535393538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000535393538 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)c(NC(=O)c3ccncc3)c(Cl)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 2, 4, 19, 19, 19, 25, 25, 19, 25, 25, 4, 4, 4, 5, 5, 10, 10, 10, 10, 10, 5, 2, 4, 19, 25, 25, 25, 25, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535393538 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535393538 Building ZINC000535410297 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535410297 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/724 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cc3ccccc3o2)cn1) `ZINC000535410297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535410297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000535410297 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cc3ccccc3o2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 8, 2, 8, 8, 8, 15, 19, 19, 31, 31, 34, 34, 34, 34, 34, 34, 34, 34, 4, 4, 6, 6, 6, 6, 6, 4, 2, 8, 8, 2, 8, 15, 15, 19, 19, 19, 34, 34, 34, 34, 34, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 128 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/725 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/725' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cc3ccccc3o2)cn1) `ZINC000535410297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535410297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000535410297 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cc3ccccc3o2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 8, 2, 8, 8, 8, 15, 21, 21, 34, 34, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 6, 6, 6, 6, 6, 4, 2, 8, 8, 2, 8, 15, 15, 21, 21, 21, 37, 37, 37, 37, 37, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 140 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535410297 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297 Building ZINC000535410297 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535410297 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 724) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cc3ccccc3o2)cn1) `ZINC000535410297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535410297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000535410297 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cc3ccccc3o2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 8, 2, 8, 8, 8, 15, 19, 19, 31, 31, 34, 34, 34, 34, 34, 34, 34, 34, 4, 4, 6, 6, 6, 6, 6, 4, 2, 8, 8, 2, 8, 15, 15, 19, 19, 19, 34, 34, 34, 34, 34, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 128 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 725) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cc3ccccc3o2)cn1) `ZINC000535410297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535410297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000535410297 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cc3ccccc3o2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 8, 2, 8, 8, 8, 15, 21, 21, 34, 34, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 6, 6, 6, 6, 6, 4, 2, 8, 8, 2, 8, 15, 15, 21, 21, 21, 37, 37, 37, 37, 37, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 140 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535410297 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535410297 Building ZINC000535432642 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535432642 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/726 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cn1) `ZINC000535432642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535432642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000535432642 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 3, 3, 3, 1, 1, 1, 1, 2, 4, 10, 10, 10, 10, 22, 22, 27, 27, 27, 27, 27, 22, 26, 26, 22, 26, 26, 26, 10, 10, 3, 3, 13, 13, 13, 13, 13, 3, 10, 10, 10, 10, 27, 27, 27, 27, 27, 26, 26, 26, 26, 10, 10, 10, 10, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/727 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cn1) `ZINC000535432642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535432642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000535432642 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 19, 19, 23, 23, 23, 23, 23, 19, 23, 23, 19, 19, 23, 23, 11, 11, 6, 6, 16, 16, 16, 16, 16, 6, 11, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535432642 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642 Building ZINC000535432642 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535432642 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 726) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cn1) `ZINC000535432642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535432642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000535432642 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 3, 3, 3, 1, 1, 1, 1, 2, 4, 10, 10, 10, 10, 22, 22, 27, 27, 27, 27, 27, 22, 26, 26, 22, 26, 26, 26, 10, 10, 3, 3, 13, 13, 13, 13, 13, 3, 10, 10, 10, 10, 27, 27, 27, 27, 27, 26, 26, 26, 26, 10, 10, 10, 10, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 727) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cn1) `ZINC000535432642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535432642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000535432642 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 19, 19, 23, 23, 23, 23, 23, 19, 23, 23, 19, 19, 23, 23, 11, 11, 6, 6, 16, 16, 16, 16, 16, 6, 11, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535432642 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432642 Building ZINC000535432643 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535432643 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/728 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cn1) `ZINC000535432643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535432643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000535432643 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 2, 2, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 23, 23, 28, 28, 23, 28, 28, 23, 28, 28, 28, 28, 28, 28, 11, 11, 2, 2, 11, 11, 11, 11, 11, 2, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/729 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/729' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cn1) `ZINC000535432643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535432643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000535432643 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 19, 19, 23, 23, 19, 23, 23, 19, 24, 24, 19, 19, 24, 24, 11, 11, 6, 6, 15, 15, 15, 15, 15, 6, 11, 11, 11, 11, 23, 23, 23, 23, 23, 24, 24, 24, 24, 11, 11, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535432643 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643 Building ZINC000535432643 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535432643 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 728) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cn1) `ZINC000535432643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535432643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000535432643 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 2, 2, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 23, 23, 28, 28, 23, 28, 28, 23, 28, 28, 28, 28, 28, 28, 11, 11, 2, 2, 11, 11, 11, 11, 11, 2, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 729) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cn1) `ZINC000535432643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535432643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000535432643 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 19, 19, 23, 23, 19, 23, 23, 19, 24, 24, 19, 19, 24, 24, 11, 11, 6, 6, 15, 15, 15, 15, 15, 6, 11, 11, 11, 11, 23, 23, 23, 23, 23, 24, 24, 24, 24, 11, 11, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535432643 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535432643 Building ZINC000535445795 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535445795 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/730 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@H](c1ccc(Br)cc1)c1cccnc1) `ZINC000535445795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535445795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000535445795 none CCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@H](c1ccc(Br)cc1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 10, 4, 6, 9, 9, 10, 10, 10, 10, 10, 10, 9, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 4, 10, 10, 10, 10, 10, 4, 10, 10, 10, 10, 21, 21, 21, 21] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/731 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/731' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@H](c1ccc(Br)cc1)c1cccnc1) `ZINC000535445795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535445795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000535445795 none CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@H](c1ccc(Br)cc1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 9, 4, 5, 8, 8, 9, 9, 8, 9, 9, 9, 8, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 4, 9, 9, 9, 9, 9, 4, 9, 9, 9, 9, 18, 18, 18, 18] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535445795 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795 Building ZINC000535445795 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535445795 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 730) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@H](c1ccc(Br)cc1)c1cccnc1) `ZINC000535445795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535445795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000535445795 none CCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@H](c1ccc(Br)cc1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 10, 4, 6, 9, 9, 10, 10, 10, 10, 10, 10, 9, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 4, 10, 10, 10, 10, 10, 4, 10, 10, 10, 10, 21, 21, 21, 21] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 731) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@H](c1ccc(Br)cc1)c1cccnc1) `ZINC000535445795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535445795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000535445795 none CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@H](c1ccc(Br)cc1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 9, 4, 5, 8, 8, 9, 9, 8, 9, 9, 9, 8, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 4, 9, 9, 9, 9, 9, 4, 9, 9, 9, 9, 18, 18, 18, 18] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535445795 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445795 Building ZINC000535445791 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535445791 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/732 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@@H](c1ccc(Br)cc1)c1cccnc1) `ZINC000535445791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535445791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000535445791 none CCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@@H](c1ccc(Br)cc1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 9, 4, 5, 8, 8, 9, 9, 9, 8, 9, 9, 8, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 4, 9, 9, 9, 9, 9, 4, 9, 9, 9, 9, 18, 18, 18, 18] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/733 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/733' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@@H](c1ccc(Br)cc1)c1cccnc1) `ZINC000535445791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535445791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000535445791 none CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@@H](c1ccc(Br)cc1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 10, 4, 6, 9, 9, 10, 10, 10, 10, 10, 10, 9, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 4, 10, 10, 10, 10, 10, 4, 10, 10, 10, 10, 20, 20, 20, 20] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 98 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535445791 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791 Building ZINC000535445791 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535445791 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 732) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@@H](c1ccc(Br)cc1)c1cccnc1) `ZINC000535445791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535445791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000535445791 none CCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@@H](c1ccc(Br)cc1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 9, 4, 5, 8, 8, 9, 9, 9, 8, 9, 9, 8, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 4, 9, 9, 9, 9, 9, 4, 9, 9, 9, 9, 18, 18, 18, 18] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 733) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@@H](c1ccc(Br)cc1)c1cccnc1) `ZINC000535445791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535445791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000535445791 none CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@@H](c1ccc(Br)cc1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 10, 4, 6, 9, 9, 10, 10, 10, 10, 10, 10, 9, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 4, 10, 10, 10, 10, 10, 4, 10, 10, 10, 10, 20, 20, 20, 20] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 98 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535445791 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535445791 Building ZINC000535450319 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535450319 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/734 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(=O)OC)ccc2Sc2ccc(Cl)cn2)cn1) `ZINC000535450319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535450319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000535450319 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(=O)OC)ccc2Sc2ccc(Cl)cn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 14, 1, 1, 1, 1, 16, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 16, 16, 16, 6, 6, 6, 6, 15, 23, 23, 23, 23, 23, 23, 6, 6, 12, 12, 12, 12, 12, 6, 4, 6, 16, 16, 16, 6, 6, 23, 23, 23, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/735 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/735' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(C(=O)OC)ccc2Sc2ccc(Cl)cn2)cn1) `ZINC000535450319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535450319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000535450319 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(C(=O)OC)ccc2Sc2ccc(Cl)cn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 14, 1, 1, 1, 1, 16, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 15, 15, 15, 6, 6, 6, 6, 16, 23, 23, 23, 23, 23, 23, 6, 6, 11, 11, 11, 11, 11, 6, 4, 6, 15, 15, 15, 6, 6, 23, 23, 23, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535450319 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319 Building ZINC000535450319 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535450319 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 734) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/734: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(=O)OC)ccc2Sc2ccc(Cl)cn2)cn1) `ZINC000535450319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535450319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000535450319 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(=O)OC)ccc2Sc2ccc(Cl)cn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 14, 1, 1, 1, 1, 16, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 16, 16, 16, 6, 6, 6, 6, 15, 23, 23, 23, 23, 23, 23, 6, 6, 12, 12, 12, 12, 12, 6, 4, 6, 16, 16, 16, 6, 6, 23, 23, 23, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 735) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/735: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(C(=O)OC)ccc2Sc2ccc(Cl)cn2)cn1) `ZINC000535450319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535450319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000535450319 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(C(=O)OC)ccc2Sc2ccc(Cl)cn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 14, 1, 1, 1, 1, 16, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 15, 15, 15, 6, 6, 6, 6, 16, 23, 23, 23, 23, 23, 23, 6, 6, 11, 11, 11, 11, 11, 6, 4, 6, 15, 15, 15, 6, 6, 23, 23, 23, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535450319 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535450319 Building ZINC000535451049 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535451049 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/736 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccccc3)cc2C(F)(F)F)cn1) `ZINC000535451049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535451049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000535451049 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccccc3)cc2C(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 3, 5, 16, 16, 16, 27, 27, 25, 27, 27, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 6, 3, 6, 6, 16, 27, 27, 27, 27, 27, 6, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/737 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/737' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccccc3)cc2C(F)(F)F)cn1) `ZINC000535451049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535451049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000535451049 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccccc3)cc2C(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 3, 5, 18, 18, 18, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 6, 3, 6, 6, 18, 31, 31, 31, 31, 31, 6, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535451049 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049 Building ZINC000535451049 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535451049 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 736) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/736: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccccc3)cc2C(F)(F)F)cn1) `ZINC000535451049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535451049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000535451049 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccccc3)cc2C(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 3, 5, 16, 16, 16, 27, 27, 25, 27, 27, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 6, 3, 6, 6, 16, 27, 27, 27, 27, 27, 6, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 737) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/737: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccccc3)cc2C(F)(F)F)cn1) `ZINC000535451049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535451049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000535451049 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccccc3)cc2C(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 3, 5, 18, 18, 18, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 6, 3, 6, 6, 18, 31, 31, 31, 31, 31, 6, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535451049 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451049 Building ZINC000535451835 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535451835 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/738 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3ccc(OC)cc3)nn2c2cccc(C)c2)cn1) `ZINC000535451835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535451835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000535451835 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3ccc(OC)cc3)nn2c2cccc(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 12, 12, 4, 4, 18, 12, 12, 4, 4, 4, 8, 8, 8, 8, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 4, 12, 12, 18, 18, 18, 12, 12, 8, 8, 8, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/739 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/739' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(c3ccc(OC)cc3)nn2c2cccc(C)c2)cn1) `ZINC000535451835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535451835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000535451835 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(c3ccc(OC)cc3)nn2c2cccc(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 12, 12, 4, 4, 17, 12, 12, 4, 4, 4, 8, 8, 8, 8, 8, 8, 5, 5, 10, 10, 10, 10, 10, 5, 2, 4, 12, 12, 17, 17, 17, 12, 12, 8, 8, 8, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535451835 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835 Building ZINC000535451835 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535451835 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 738) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/738: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3ccc(OC)cc3)nn2c2cccc(C)c2)cn1) `ZINC000535451835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535451835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000535451835 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3ccc(OC)cc3)nn2c2cccc(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 12, 12, 4, 4, 18, 12, 12, 4, 4, 4, 8, 8, 8, 8, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 4, 12, 12, 18, 18, 18, 12, 12, 8, 8, 8, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 739) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/739: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(c3ccc(OC)cc3)nn2c2cccc(C)c2)cn1) `ZINC000535451835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535451835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000535451835 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(c3ccc(OC)cc3)nn2c2cccc(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 12, 12, 4, 4, 17, 12, 12, 4, 4, 4, 8, 8, 8, 8, 8, 8, 5, 5, 10, 10, 10, 10, 10, 5, 2, 4, 12, 12, 17, 17, 17, 12, 12, 8, 8, 8, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535451835 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535451835 Building ZINC000535529326 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535529326 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/740 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)nc1) `ZINC000535529326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535529326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000535529326 none CC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 3, 14, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 14, 14, 14, 3, 3, 2, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/741 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/741' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)nc1) `ZINC000535529326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535529326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000535529326 none CC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 3, 14, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 2, 2, 3, 3, 14, 14, 14, 3, 3, 2, 2, 2, 2, 13, 13, 2, 13, 2, 2, 2, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535529326 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326 Building ZINC000535529326 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535529326 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 740) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/740: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)nc1) `ZINC000535529326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535529326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000535529326 none CC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 3, 14, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 14, 14, 14, 3, 3, 2, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 741) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)nc1) `ZINC000535529326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535529326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000535529326 none CC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 3, 14, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 2, 2, 3, 3, 14, 14, 14, 3, 3, 2, 2, 2, 2, 13, 13, 2, 13, 2, 2, 2, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535529326 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535529326 Building ZINC000535517750 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535517750 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/742 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2nc(C)c(c3nc4ccccc4n3C(F)F)s2)cn1) `ZINC000535517750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535517750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000535517750 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2nc(C)c(c3nc4ccccc4n3C(F)F)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'F', 'F', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 15, 15, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 33, 33, 4, 5, 5, 10, 10, 10, 10, 10, 5, 2, 4, 4, 4, 19, 19, 19, 19, 33, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/743 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/743' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2nc(C)c(c3nc4ccccc4n3C(F)F)s2)cn1) `ZINC000535517750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535517750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000535517750 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2nc(C)c(c3nc4ccccc4n3C(F)F)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'F', 'F', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 15, 15, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 36, 36, 4, 5, 5, 12, 12, 12, 12, 12, 5, 2, 4, 4, 4, 18, 18, 18, 18, 36, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535517750 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750 Building ZINC000535517750 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535517750 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 742) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2nc(C)c(c3nc4ccccc4n3C(F)F)s2)cn1) `ZINC000535517750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535517750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000535517750 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2nc(C)c(c3nc4ccccc4n3C(F)F)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'F', 'F', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 15, 15, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 33, 33, 4, 5, 5, 10, 10, 10, 10, 10, 5, 2, 4, 4, 4, 19, 19, 19, 19, 33, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 743) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/743: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2nc(C)c(c3nc4ccccc4n3C(F)F)s2)cn1) `ZINC000535517750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535517750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000535517750 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2nc(C)c(c3nc4ccccc4n3C(F)F)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'F', 'F', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 15, 15, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 36, 36, 4, 5, 5, 12, 12, 12, 12, 12, 5, 2, 4, 4, 4, 18, 18, 18, 18, 36, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535517750 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535517750 Building ZINC000535553677 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535553677 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/744 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000535553677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535553677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000535553677 none CCC[C@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 27, 18, 27, 27, 15, 10, 15, 15, 7, 7, 3, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 28, 28, 28, 28, 28, 28, 28, 27, 27, 27, 18, 10, 10, 3, 7, 7, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/745 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/745' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000535553677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535553677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000535553677 none CCC[C@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 24, 17, 24, 24, 14, 9, 14, 14, 7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 25, 25, 25, 25, 25, 25, 25, 24, 24, 24, 17, 9, 9, 7, 7, 7, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535553677 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677 Building ZINC000535553677 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000535553677 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 744) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000535553677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000535553677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000535553677 none CCC[C@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 27, 18, 27, 27, 15, 10, 15, 15, 7, 7, 3, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 28, 28, 28, 28, 28, 28, 28, 27, 27, 27, 18, 10, 10, 3, 7, 7, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 745) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000535553677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000535553677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000535553677 none CCC[C@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 24, 17, 24, 24, 14, 9, 14, 14, 7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 25, 25, 25, 25, 25, 25, 25, 24, 24, 24, 17, 9, 9, 7, 7, 7, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000535553677 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000535553677 Building ZINC000428784315 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428784315 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/746 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCNC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)ccc1Cl) `ZINC000428784315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428784315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000428784315 none CCN(CC)CCNC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 50, 50, 36, 12, 12, 7, 12, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 36, 36, 12, 7, 2, 2, 2, 7, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/747 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/747' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCNC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)ccc1Cl) `ZINC000428784315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428784315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000428784315 none CCN(CC)CCNC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 50, 50, 36, 11, 11, 6, 11, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 36, 36, 11, 6, 2, 2, 2, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000428784315 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315 Building ZINC000428784315 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428784315 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 746) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/746: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCNC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)ccc1Cl) `ZINC000428784315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428784315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000428784315 none CCN(CC)CCNC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 50, 50, 36, 12, 12, 7, 12, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 36, 36, 12, 7, 2, 2, 2, 7, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 747) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/747: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCNC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)ccc1Cl) `ZINC000428784315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428784315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000428784315 none CCN(CC)CCNC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 50, 50, 36, 11, 11, 6, 11, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 36, 36, 11, 6, 2, 2, 2, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000428784315 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428784315 Building ZINC000518797832 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000518797832 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/748 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(C4CC4)cc32)C1) `ZINC000518797832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000518797832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000518797832 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(C4CC4)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 8, 23, 24, 39, 39, 39, 39, 39, 39, 39, 39, 39, 50, 50, 39, 39, 5, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 50, 50, 50, 50, 50, 39, 5, 5] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 128 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/749 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/749' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(C4CC4)cc32)C1) `ZINC000518797832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000518797832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000518797832 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(C4CC4)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 8, 23, 25, 36, 36, 36, 36, 36, 36, 36, 36, 36, 50, 50, 36, 36, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 50, 50, 50, 50, 50, 36, 6, 6] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000518797832 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832 Building ZINC000518797832 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000518797832 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 748) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/748: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(C4CC4)cc32)C1) `ZINC000518797832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000518797832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000518797832 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(C4CC4)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 8, 23, 24, 39, 39, 39, 39, 39, 39, 39, 39, 39, 50, 50, 39, 39, 5, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 50, 50, 50, 50, 50, 39, 5, 5] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 128 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 749) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/749: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(C4CC4)cc32)C1) `ZINC000518797832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000518797832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000518797832 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(C4CC4)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 8, 23, 25, 36, 36, 36, 36, 36, 36, 36, 36, 36, 50, 50, 36, 36, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 50, 50, 50, 50, 50, 36, 6, 6] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000518797832 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000518797832 Building ZINC000504535032 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000504535032 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/750 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)cc1) `ZINC000504535032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000504535032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000504535032 none COc1ccc(NC(=O)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 12, 12, 2, 12, 2, 7, 7, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 31, 31, 31, 31, 31, 31, 31, 12, 7, 7, 2, 5, 5, 5, 5, 5, 5, 5, 7, 7, 31, 31] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/751 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/751' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)c2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)cc1) `ZINC000504535032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000504535032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000504535032 none COc1ccc(NC(=O)c2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 14, 14, 2, 14, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 32, 32, 32, 32, 32, 32, 32, 14, 9, 9, 2, 5, 5, 5, 5, 5, 5, 5, 9, 9, 32, 32] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000504535032 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032 Building ZINC000504535032 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000504535032 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 750) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)cc1) `ZINC000504535032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000504535032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000504535032 none COc1ccc(NC(=O)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 12, 12, 2, 12, 2, 7, 7, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 31, 31, 31, 31, 31, 31, 31, 12, 7, 7, 2, 5, 5, 5, 5, 5, 5, 5, 7, 7, 31, 31] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 751) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)c2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)cc1) `ZINC000504535032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000504535032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000504535032 none COc1ccc(NC(=O)c2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 14, 14, 2, 14, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 32, 32, 32, 32, 32, 32, 32, 14, 9, 9, 2, 5, 5, 5, 5, 5, 5, 5, 9, 9, 32, 32] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000504535032 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000504535032 Building ZINC000539659491 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000539659491 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/752 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncc(Br)cc2I)cc1) `ZINC000539659491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000539659491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000539659491 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncc(Br)cc2I)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 17, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 10, 24, 24, 6, 6] 29 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/753 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/753' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncc(Br)cc2I)cc1) `ZINC000539659491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000539659491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000539659491 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncc(Br)cc2I)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 17, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 10, 24, 24, 6, 6] 28 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000539659491 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491 Building ZINC000539659491 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000539659491 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 752) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/752: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncc(Br)cc2I)cc1) `ZINC000539659491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000539659491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000539659491 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncc(Br)cc2I)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 17, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 10, 24, 24, 6, 6] 29 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 753) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/753: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncc(Br)cc2I)cc1) `ZINC000539659491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000539659491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000539659491 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncc(Br)cc2I)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 17, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 10, 24, 24, 6, 6] 28 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000539659491 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539659491 Building ZINC000539742833 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000539742833 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/754 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000539742833.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000539742833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000539742833 none O=C(N1CCC[C@@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 6, 1, 5, 5, 5, 5, 5, 5, 8, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 21, 42, 42, 42, 42, 42, 20, 2, 1, 1, 1, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 2, 2, 2, 2, 2, 2, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 2, 2, 3, 5, 5, 3, 5, 5, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/755 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/755' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000539742833.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000539742833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000539742833 none O=C(N1CCC[C@@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 6, 1, 5, 5, 5, 5, 5, 5, 8, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 23, 40, 40, 40, 40, 40, 20, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 2, 2, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000539742833 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833 Building ZINC000539742833 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000539742833 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 754) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/754: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000539742833.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000539742833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000539742833 none O=C(N1CCC[C@@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 6, 1, 5, 5, 5, 5, 5, 5, 8, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 21, 42, 42, 42, 42, 42, 20, 2, 1, 1, 1, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 2, 2, 2, 2, 2, 2, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 2, 2, 3, 5, 5, 3, 5, 5, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 755) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/755: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000539742833.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000539742833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000539742833 none O=C(N1CCC[C@@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 6, 1, 5, 5, 5, 5, 5, 5, 8, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 23, 40, 40, 40, 40, 40, 20, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 2, 2, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000539742833 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742833 Building ZINC000539742835 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000539742835 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/756 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000539742835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000539742835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000539742835 none O=C(N1CCC[C@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 6, 1, 5, 5, 5, 5, 5, 5, 8, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 22, 41, 41, 41, 41, 41, 19, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 2, 2, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/757 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/757' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000539742835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000539742835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000539742835 none O=C(N1CCC[C@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 6, 1, 5, 5, 5, 5, 5, 5, 8, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 25, 41, 41, 41, 41, 41, 23, 3, 1, 1, 1, 3, 3, 3, 3, 4, 4, 3, 4, 4, 3, 3, 3, 3, 3, 3, 3, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 3, 3, 3, 4, 4, 3, 4, 4, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000539742835 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835 Building ZINC000539742835 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000539742835 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 756) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000539742835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000539742835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000539742835 none O=C(N1CCC[C@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 6, 1, 5, 5, 5, 5, 5, 5, 8, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 22, 41, 41, 41, 41, 41, 19, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 2, 2, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 757) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/757: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000539742835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000539742835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000539742835 none O=C(N1CCC[C@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 6, 1, 5, 5, 5, 5, 5, 5, 8, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 25, 41, 41, 41, 41, 41, 23, 3, 1, 1, 1, 3, 3, 3, 3, 4, 4, 3, 4, 4, 3, 3, 3, 3, 3, 3, 3, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 3, 3, 3, 4, 4, 3, 4, 4, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000539742835 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539742835 Building ZINC000539746060 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000539746060 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/758 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1) `ZINC000539746060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000539746060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000539746060 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 4, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 2, 5, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 11, 11, 8, 11, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 55 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/759 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1) `ZINC000539746060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000539746060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000539746060 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 5, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 42 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/760 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/760' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1) `ZINC000539746060.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000539746060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000539746060 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 4, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 2, 5, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 11, 11, 8, 11, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 55 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/761 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/761' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1) `ZINC000539746060.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000539746060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000539746060 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 5, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 42 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000539746060 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 Building ZINC000539746060 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000539746060 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 758) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/758: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1) `ZINC000539746060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000539746060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000539746060 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 4, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 2, 5, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 11, 11, 8, 11, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 55 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 759) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/759: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1) `ZINC000539746060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000539746060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000539746060 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 5, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 42 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 760) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1) `ZINC000539746060.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000539746060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000539746060 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 4, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 2, 5, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 11, 11, 8, 11, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 55 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 761) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1) `ZINC000539746060.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000539746060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000539746060 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 5, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 42 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000539746060 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 Building ZINC000539746060 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000539746060 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 758) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/758: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1) `ZINC000539746060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000539746060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000539746060 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 4, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 2, 5, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 11, 11, 8, 11, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 55 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 759) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/759: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1) `ZINC000539746060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000539746060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000539746060 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 5, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 42 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 760) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1) `ZINC000539746060.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000539746060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000539746060 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 4, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 2, 5, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 11, 11, 8, 11, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 55 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 761) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1) `ZINC000539746060.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000539746060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000539746060 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 5, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 42 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000539746060 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 Building ZINC000539746060 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000539746060 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 758) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/758: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1) `ZINC000539746060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000539746060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000539746060 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 4, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 2, 5, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 11, 11, 8, 11, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 55 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 759) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/759: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1) `ZINC000539746060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000539746060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000539746060 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 5, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 42 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 760) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1) `ZINC000539746060.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000539746060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000539746060 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 4, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 2, 5, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 11, 11, 8, 11, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 55 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 761) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1) `ZINC000539746060.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000539746060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000539746060 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC2(CCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 5, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 42 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000539746060 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539746060 Building ZINC000546893728 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546893728 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/762 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cc(Br)cnc1OCC(F)(F)F) `ZINC000546893728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546893728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000546893728 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cc(Br)cnc1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 8, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 30, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 4, 8, 8, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/763 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/763' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cc(Br)cnc1OCC(F)(F)F) `ZINC000546893728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546893728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000546893728 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cc(Br)cnc1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 8, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 30, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 4, 8, 8, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000546893728 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728 Building ZINC000546893728 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546893728 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 762) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/762: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cc(Br)cnc1OCC(F)(F)F) `ZINC000546893728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546893728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000546893728 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cc(Br)cnc1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 8, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 30, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 4, 8, 8, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 763) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/763: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cc(Br)cnc1OCC(F)(F)F) `ZINC000546893728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546893728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000546893728 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cc(Br)cnc1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 8, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 30, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 4, 8, 8, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000546893728 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546893728 Building ZINC000539918807 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000539918807 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/764 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1COC1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000539918807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000539918807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000539918807 none COc1ccccc1COC1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 42, 42, 42, 42, 42, 42, 17, 7, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 46, 46, 46, 42, 42, 42, 42, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/765 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/765' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1COC1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000539918807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000539918807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000539918807 none COc1ccccc1COC1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 37, 37, 37, 37, 37, 37, 13, 6, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 3, 3, 43, 43, 43, 37, 37, 37, 37, 13, 13, 3, 3, 3, 3, 3, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000539918807 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807 Building ZINC000539918807 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000539918807 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 764) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/764: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1COC1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000539918807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000539918807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000539918807 none COc1ccccc1COC1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 42, 42, 42, 42, 42, 42, 17, 7, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 46, 46, 46, 42, 42, 42, 42, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 765) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/765: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1COC1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000539918807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000539918807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000539918807 none COc1ccccc1COC1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 37, 37, 37, 37, 37, 37, 13, 6, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 3, 3, 43, 43, 43, 37, 37, 37, 37, 13, 13, 3, 3, 3, 3, 3, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000539918807 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000539918807 Building ZINC000505415524 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000505415524 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/766 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCc1cc(c2ccccc2)n(C)n1)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000505415524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000505415524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000505415524 none CN(CCCc1cc(c2ccccc2)n(C)n1)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 10, 16, 39, 39, 39, 42, 42, 41, 42, 42, 39, 39, 39, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 6, 6, 11, 11, 16, 16, 39, 42, 42, 41, 42, 42, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/767 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/767' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCc1cc(c2ccccc2)n(C)n1)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000505415524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000505415524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000505415524 none CN(CCCc1cc(c2ccccc2)n(C)n1)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 10, 16, 38, 38, 38, 41, 41, 38, 41, 41, 38, 38, 38, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 6, 6, 11, 11, 16, 16, 38, 41, 41, 38, 41, 41, 38, 38, 38, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000505415524 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524 Building ZINC000505415524 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000505415524 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 766) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/766: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCc1cc(c2ccccc2)n(C)n1)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000505415524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000505415524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000505415524 none CN(CCCc1cc(c2ccccc2)n(C)n1)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 10, 16, 39, 39, 39, 42, 42, 41, 42, 42, 39, 39, 39, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 6, 6, 11, 11, 16, 16, 39, 42, 42, 41, 42, 42, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 767) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/767: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCc1cc(c2ccccc2)n(C)n1)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000505415524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000505415524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000505415524 none CN(CCCc1cc(c2ccccc2)n(C)n1)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 10, 16, 38, 38, 38, 41, 41, 38, 41, 41, 38, 38, 38, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 6, 6, 11, 11, 16, 16, 38, 41, 41, 38, 41, 41, 38, 38, 38, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000505415524 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000505415524 Building ZINC000546895729 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546895729 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/768 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Br)c(OC)c(OC)c2)cc1Cl) `ZINC000546895729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546895729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000546895729 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Br)c(OC)c(OC)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 12, 5, 1, 12, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 23, 13, 13, 26, 13, 2, 2, 2, 4, 4, 4, 2, 2, 1, 6, 6, 13, 23, 23, 23, 26, 26, 26, 13, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/769 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/769' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(Br)c(OC)c(OC)c2)cc1Cl) `ZINC000546895729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546895729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000546895729 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(Br)c(OC)c(OC)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 12, 5, 1, 12, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 23, 13, 13, 26, 13, 2, 2, 2, 4, 4, 4, 2, 2, 1, 6, 6, 13, 23, 23, 23, 26, 26, 26, 13, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000546895729 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729 Building ZINC000546895729 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546895729 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 768) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Br)c(OC)c(OC)c2)cc1Cl) `ZINC000546895729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546895729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000546895729 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Br)c(OC)c(OC)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 12, 5, 1, 12, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 23, 13, 13, 26, 13, 2, 2, 2, 4, 4, 4, 2, 2, 1, 6, 6, 13, 23, 23, 23, 26, 26, 26, 13, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 769) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(Br)c(OC)c(OC)c2)cc1Cl) `ZINC000546895729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546895729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000546895729 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(Br)c(OC)c(OC)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 12, 5, 1, 12, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 23, 13, 13, 26, 13, 2, 2, 2, 4, 4, 4, 2, 2, 1, 6, 6, 13, 23, 23, 23, 26, 26, 26, 13, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000546895729 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000546895729 Building ZINC001272320941 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001272320941 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/770 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nnn1CCOc1ccc(F)cc1) `ZINC001272320941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001272320941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001272320941 none Cc1c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nnn1CCOc1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 8, 8, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 4, 4, 4, 14, 20, 40, 41, 41, 40, 41, 41, 41, 4, 4, 4, 2, 3, 1, 3, 14, 14, 20, 20, 41, 41, 41, 41] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/771 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/771' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nnn1CCOc1ccc(F)cc1) `ZINC001272320941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001272320941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001272320941 none Cc1c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nnn1CCOc1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 8, 8, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 4, 4, 4, 14, 20, 40, 41, 41, 40, 41, 41, 41, 4, 4, 4, 2, 3, 1, 3, 14, 14, 20, 20, 41, 41, 41, 41] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC001272320941 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941 Building ZINC001272320941 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001272320941 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 770) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/770: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nnn1CCOc1ccc(F)cc1) `ZINC001272320941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001272320941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001272320941 none Cc1c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nnn1CCOc1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 8, 8, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 4, 4, 4, 14, 20, 40, 41, 41, 40, 41, 41, 41, 4, 4, 4, 2, 3, 1, 3, 14, 14, 20, 20, 41, 41, 41, 41] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 771) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/771: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nnn1CCOc1ccc(F)cc1) `ZINC001272320941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001272320941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001272320941 none Cc1c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nnn1CCOc1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 8, 8, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 4, 4, 4, 14, 20, 40, 41, 41, 40, 41, 41, 41, 4, 4, 4, 2, 3, 1, 3, 14, 14, 20, 20, 41, 41, 41, 41] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC001272320941 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC001272320941 Building ZINC000540003104 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540003104 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/772 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](COc2cccc(F)c2)c2cccc(C(F)(F)F)c2)cn1) `ZINC000540003104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540003104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540003104 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](COc2cccc(F)c2)c2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 4, 4, 7, 13, 21, 21, 21, 21, 21, 21, 4, 9, 9, 7, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 3, 7, 7, 21, 21, 21, 21, 9, 9, 7, 9, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/773 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/773' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](COc2cccc(F)c2)c2cccc(C(F)(F)F)c2)cn1) `ZINC000540003104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540003104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540003104 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](COc2cccc(F)c2)c2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 7, 14, 22, 22, 22, 22, 22, 22, 5, 8, 8, 7, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 3, 7, 7, 22, 22, 22, 22, 8, 8, 7, 8, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540003104 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104 Building ZINC000540003104 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540003104 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 772) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](COc2cccc(F)c2)c2cccc(C(F)(F)F)c2)cn1) `ZINC000540003104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540003104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540003104 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](COc2cccc(F)c2)c2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 4, 4, 7, 13, 21, 21, 21, 21, 21, 21, 4, 9, 9, 7, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 3, 7, 7, 21, 21, 21, 21, 9, 9, 7, 9, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 773) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](COc2cccc(F)c2)c2cccc(C(F)(F)F)c2)cn1) `ZINC000540003104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540003104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540003104 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](COc2cccc(F)c2)c2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 7, 14, 22, 22, 22, 22, 22, 22, 5, 8, 8, 7, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 3, 7, 7, 22, 22, 22, 22, 8, 8, 7, 8, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540003104 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003104 Building ZINC000540003106 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540003106 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/774 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](COc2cccc(F)c2)c2cccc(C(F)(F)F)c2)cn1) `ZINC000540003106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540003106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540003106 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](COc2cccc(F)c2)c2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 9, 15, 24, 24, 24, 24, 24, 24, 5, 9, 9, 7, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 4, 3, 9, 9, 24, 24, 24, 24, 9, 9, 7, 9, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 82 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/775 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/775' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](COc2cccc(F)c2)c2cccc(C(F)(F)F)c2)cn1) `ZINC000540003106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540003106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540003106 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](COc2cccc(F)c2)c2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 7, 13, 21, 21, 21, 21, 21, 21, 5, 11, 11, 9, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 3, 7, 7, 21, 21, 21, 21, 11, 11, 9, 11, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540003106 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106 Building ZINC000540003106 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540003106 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 774) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/774: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](COc2cccc(F)c2)c2cccc(C(F)(F)F)c2)cn1) `ZINC000540003106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540003106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540003106 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](COc2cccc(F)c2)c2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 9, 15, 24, 24, 24, 24, 24, 24, 5, 9, 9, 7, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 4, 3, 9, 9, 24, 24, 24, 24, 9, 9, 7, 9, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 82 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 775) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/775: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](COc2cccc(F)c2)c2cccc(C(F)(F)F)c2)cn1) `ZINC000540003106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540003106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540003106 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](COc2cccc(F)c2)c2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 7, 13, 21, 21, 21, 21, 21, 21, 5, 11, 11, 9, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 3, 7, 7, 21, 21, 21, 21, 11, 11, 9, 11, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540003106 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540003106 Building ZINC000462841567 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000462841567 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/776 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)n2)c1) `ZINC000462841567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000462841567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000462841567 none COc1cc(OC)cc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 19, 5, 19, 19, 25, 19, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 19, 26, 26, 26, 5, 25, 25, 25, 19, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 19] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/777 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/777' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)n2)c1) `ZINC000462841567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000462841567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000462841567 none COc1cc(OC)cc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 19, 4, 19, 19, 26, 19, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 19, 25, 25, 25, 5, 26, 26, 26, 19, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 19] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000462841567 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567 Building ZINC000462841567 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000462841567 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 776) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/776: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)n2)c1) `ZINC000462841567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000462841567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000462841567 none COc1cc(OC)cc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 19, 5, 19, 19, 25, 19, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 19, 26, 26, 26, 5, 25, 25, 25, 19, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 19] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 777) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/777: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)n2)c1) `ZINC000462841567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000462841567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000462841567 none COc1cc(OC)cc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 19, 4, 19, 19, 26, 19, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 19, 25, 25, 25, 5, 26, 26, 26, 19, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 19] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000462841567 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462841567 Building ZINC000540025166 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540025166 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/778 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccc(C(F)(F)F)cc1) `ZINC000540025166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540025166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000540025166 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 6, 6, 6, 11, 11, 25, 11, 24, 24, 11, 13, 24, 24, 24, 24, 24, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 6, 25, 25, 75, 24, 24, 24, 24] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 301 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/779 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/779' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccc(C(F)(F)F)cc1) `ZINC000540025166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540025166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000540025166 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 6, 6, 6, 11, 11, 26, 11, 25, 25, 11, 15, 25, 25, 25, 25, 25, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 6, 26, 26, 78, 25, 25, 25, 25] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 297 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540025166 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166 Building ZINC000540025166 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540025166 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 778) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/778: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccc(C(F)(F)F)cc1) `ZINC000540025166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540025166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000540025166 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 6, 6, 6, 11, 11, 25, 11, 24, 24, 11, 13, 24, 24, 24, 24, 24, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 6, 25, 25, 75, 24, 24, 24, 24] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 301 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 779) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/779: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccc(C(F)(F)F)cc1) `ZINC000540025166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540025166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000540025166 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 6, 6, 6, 11, 11, 26, 11, 25, 25, 11, 15, 25, 25, 25, 25, 25, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 6, 26, 26, 78, 25, 25, 25, 25] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 297 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540025166 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025166 Building ZINC000540025169 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540025169 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/780 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccc(C(F)(F)F)cc1) `ZINC000540025169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540025169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000540025169 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 6, 6, 6, 11, 11, 29, 11, 25, 25, 11, 11, 25, 25, 25, 25, 25, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 6, 29, 29, 87, 25, 25, 25, 25] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 339 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/781 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/781' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccc(C(F)(F)F)cc1) `ZINC000540025169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540025169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000540025169 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 7, 7, 5, 7, 7, 4, 4, 1, 1, 1, 1, 6, 6, 6, 9, 9, 22, 9, 21, 21, 9, 11, 21, 21, 21, 21, 21, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 6, 22, 22, 66, 21, 21, 21, 21] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 268 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540025169 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169 Building ZINC000540025169 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540025169 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 780) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccc(C(F)(F)F)cc1) `ZINC000540025169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540025169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000540025169 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 6, 6, 6, 11, 11, 29, 11, 25, 25, 11, 11, 25, 25, 25, 25, 25, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 6, 29, 29, 87, 25, 25, 25, 25] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 339 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 781) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccc(C(F)(F)F)cc1) `ZINC000540025169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540025169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000540025169 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 7, 7, 5, 7, 7, 4, 4, 1, 1, 1, 1, 6, 6, 6, 9, 9, 22, 9, 21, 21, 9, 11, 21, 21, 21, 21, 21, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 6, 22, 22, 66, 21, 21, 21, 21] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 268 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540025169 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540025169 Building ZINC000462895335 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000462895335 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/782 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@](CO)(Cc2ccccc2)C1) `ZINC000462895335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000462895335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000462895335 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@](CO)(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 2, 8, 10, 12, 12, 12, 12, 12, 18, 12, 33, 33, 33, 33, 33, 33, 12, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 12, 12, 12, 12, 12, 12, 18, 18, 54, 33, 33, 33, 33, 33, 33, 33, 12, 12] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 222 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/783 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/783' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@](CO)(Cc2ccccc2)C1) `ZINC000462895335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000462895335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000462895335 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@](CO)(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 2, 8, 10, 13, 13, 13, 13, 13, 20, 13, 31, 31, 31, 31, 31, 31, 13, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 3, 13, 13, 13, 13, 13, 13, 20, 20, 60, 31, 31, 31, 31, 31, 31, 31, 13, 13] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 227 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000462895335 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335 Building ZINC000462895335 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000462895335 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 782) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/782: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@](CO)(Cc2ccccc2)C1) `ZINC000462895335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000462895335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000462895335 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@](CO)(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 2, 8, 10, 12, 12, 12, 12, 12, 18, 12, 33, 33, 33, 33, 33, 33, 12, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 12, 12, 12, 12, 12, 12, 18, 18, 54, 33, 33, 33, 33, 33, 33, 33, 12, 12] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 222 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 783) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/783: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@](CO)(Cc2ccccc2)C1) `ZINC000462895335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000462895335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000462895335 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@](CO)(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 2, 8, 10, 13, 13, 13, 13, 13, 20, 13, 31, 31, 31, 31, 31, 31, 13, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 3, 13, 13, 13, 13, 13, 13, 20, 20, 60, 31, 31, 31, 31, 31, 31, 31, 13, 13] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 227 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000462895335 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895335 Building ZINC000462895336 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000462895336 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/784 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@](CO)(Cc2ccccc2)C1) `ZINC000462895336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000462895336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000462895336 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@](CO)(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 5, 9, 9, 3, 3, 1, 1, 1, 2, 7, 9, 13, 13, 13, 13, 13, 19, 13, 32, 32, 32, 32, 32, 32, 13, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 13, 13, 13, 13, 13, 13, 19, 19, 57, 32, 32, 32, 32, 32, 32, 32, 13, 13] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 220 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/785 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/785' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@](CO)(Cc2ccccc2)C1) `ZINC000462895336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000462895336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000462895336 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@](CO)(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 1, 1, 1, 2, 8, 10, 12, 12, 12, 12, 12, 17, 12, 31, 31, 31, 31, 31, 31, 12, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 12, 12, 12, 12, 12, 12, 17, 17, 51, 31, 31, 31, 31, 31, 31, 31, 12, 12] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 192 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000462895336 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336 Building ZINC000462895336 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000462895336 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 784) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@](CO)(Cc2ccccc2)C1) `ZINC000462895336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000462895336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000462895336 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@](CO)(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 5, 9, 9, 3, 3, 1, 1, 1, 2, 7, 9, 13, 13, 13, 13, 13, 19, 13, 32, 32, 32, 32, 32, 32, 13, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 13, 13, 13, 13, 13, 13, 19, 19, 57, 32, 32, 32, 32, 32, 32, 32, 13, 13] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 220 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 785) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@](CO)(Cc2ccccc2)C1) `ZINC000462895336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000462895336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000462895336 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@](CO)(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 1, 1, 1, 2, 8, 10, 12, 12, 12, 12, 12, 17, 12, 31, 31, 31, 31, 31, 31, 12, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 12, 12, 12, 12, 12, 12, 17, 17, 51, 31, 31, 31, 31, 31, 31, 31, 12, 12] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 192 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000462895336 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000462895336 Building ZINC000540118322 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540118322 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/786 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2ccccc2n1C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1) `ZINC000540118322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540118322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000540118322 none CCc1nc2ccccc2n1C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 12, 12, 12, 12, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 12, 12, 25, 25, 25, 25, 25, 15, 15, 15, 15, 12, 12, 12, 12, 12, 6, 11, 11, 6, 11, 11, 6, 12, 12, 12, 12] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 109 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/787 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/787' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2ccccc2n1C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1) `ZINC000540118322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540118322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000540118322 none CCc1nc2ccccc2n1C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 16, 16, 16, 16, 16, 16, 16, 16, 16, 12, 12, 12, 12, 7, 2, 8, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 12, 12, 28, 28, 28, 28, 28, 16, 16, 16, 16, 12, 12, 12, 12, 12, 6, 11, 11, 6, 11, 11, 6, 12, 12, 12, 12] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 118 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540118322 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322 Building ZINC000540118322 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540118322 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 786) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/786: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2ccccc2n1C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1) `ZINC000540118322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540118322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000540118322 none CCc1nc2ccccc2n1C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 12, 12, 12, 12, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 12, 12, 25, 25, 25, 25, 25, 15, 15, 15, 15, 12, 12, 12, 12, 12, 6, 11, 11, 6, 11, 11, 6, 12, 12, 12, 12] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 109 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 787) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/787: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2ccccc2n1C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1) `ZINC000540118322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540118322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000540118322 none CCc1nc2ccccc2n1C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 16, 16, 16, 16, 16, 16, 16, 16, 16, 12, 12, 12, 12, 7, 2, 8, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 12, 12, 28, 28, 28, 28, 28, 16, 16, 16, 16, 12, 12, 12, 12, 12, 6, 11, 11, 6, 11, 11, 6, 12, 12, 12, 12] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 118 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540118322 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540118322 Building ZINC000540243730 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540243730 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/788 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540243730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540243730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540243730 none CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 11, 21, 21, 21, 21, 21, 21, 21, 21, 3, 11, 11, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 9, 9, 8, 9, 9, 8, 25, 25, 25, 21, 21, 21, 21, 11, 11, 11, 3, 8, 9, 9, 8, 9, 9, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/789 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540243730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540243730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540243730 none CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 22, 12, 22, 22, 22, 22, 22, 22, 22, 22, 3, 12, 12, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 9, 9, 8, 9, 9, 8, 25, 25, 25, 22, 22, 22, 22, 12, 12, 12, 3, 8, 9, 9, 8, 9, 9, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540243730 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730 Building ZINC000540243730 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540243730 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 788) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/788: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540243730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540243730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540243730 none CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 11, 21, 21, 21, 21, 21, 21, 21, 21, 3, 11, 11, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 9, 9, 8, 9, 9, 8, 25, 25, 25, 21, 21, 21, 21, 11, 11, 11, 3, 8, 9, 9, 8, 9, 9, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 789) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/789: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540243730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540243730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540243730 none CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 22, 12, 22, 22, 22, 22, 22, 22, 22, 22, 3, 12, 12, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 9, 9, 8, 9, 9, 8, 25, 25, 25, 22, 22, 22, 22, 12, 12, 12, 3, 8, 9, 9, 8, 9, 9, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540243730 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243730 Building ZINC000540243731 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540243731 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/790 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540243731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540243731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540243731 none CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 22, 7, 22, 22, 22, 22, 22, 22, 22, 22, 3, 7, 7, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 27, 27, 27, 22, 22, 22, 22, 7, 7, 7, 3, 7, 8, 8, 7, 8, 8, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/791 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540243731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540243731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540243731 none CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 22, 10, 22, 22, 22, 22, 22, 22, 22, 22, 4, 10, 10, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 9, 9, 7, 9, 9, 7, 27, 27, 27, 22, 22, 22, 22, 10, 10, 10, 4, 7, 9, 9, 7, 9, 9, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540243731 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731 Building ZINC000540243731 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540243731 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 790) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/790: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540243731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540243731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540243731 none CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 22, 7, 22, 22, 22, 22, 22, 22, 22, 22, 3, 7, 7, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 27, 27, 27, 22, 22, 22, 22, 7, 7, 7, 3, 7, 8, 8, 7, 8, 8, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 791) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/791: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540243731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540243731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540243731 none CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 22, 10, 22, 22, 22, 22, 22, 22, 22, 22, 4, 10, 10, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 9, 9, 7, 9, 9, 7, 27, 27, 27, 22, 22, 22, 22, 10, 10, 10, 4, 7, 9, 9, 7, 9, 9, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540243731 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243731 Building ZINC000540243732 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540243732 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/792 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540243732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540243732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540243732 none CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 22, 10, 22, 22, 22, 22, 22, 22, 22, 22, 4, 10, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 27, 27, 27, 22, 22, 22, 22, 10, 10, 10, 4, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/793 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/793' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540243732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540243732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540243732 none CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 22, 7, 22, 22, 22, 22, 22, 22, 22, 22, 3, 7, 7, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 27, 27, 27, 22, 22, 22, 22, 7, 7, 7, 3, 7, 8, 8, 7, 8, 8, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540243732 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732 Building ZINC000540243732 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540243732 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 792) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/792: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540243732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540243732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540243732 none CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 22, 10, 22, 22, 22, 22, 22, 22, 22, 22, 4, 10, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 27, 27, 27, 22, 22, 22, 22, 10, 10, 10, 4, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 793) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/793: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540243732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540243732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540243732 none CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 22, 7, 22, 22, 22, 22, 22, 22, 22, 22, 3, 7, 7, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 27, 27, 27, 22, 22, 22, 22, 7, 7, 7, 3, 7, 8, 8, 7, 8, 8, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540243732 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243732 Building ZINC000540243733 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540243733 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/794 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540243733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540243733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540243733 none CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 22, 12, 22, 22, 22, 22, 22, 22, 22, 22, 3, 12, 12, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 9, 9, 8, 9, 9, 8, 25, 25, 25, 22, 22, 22, 22, 12, 12, 12, 3, 8, 9, 9, 8, 9, 9, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/795 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/795' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540243733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540243733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540243733 none CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 11, 21, 21, 21, 21, 21, 21, 21, 21, 3, 11, 11, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 9, 9, 8, 9, 9, 8, 25, 25, 25, 21, 21, 21, 21, 11, 11, 11, 3, 8, 9, 9, 8, 9, 9, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540243733 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733 Building ZINC000540243733 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540243733 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 794) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540243733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540243733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540243733 none CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 22, 12, 22, 22, 22, 22, 22, 22, 22, 22, 3, 12, 12, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 9, 9, 8, 9, 9, 8, 25, 25, 25, 22, 22, 22, 22, 12, 12, 12, 3, 8, 9, 9, 8, 9, 9, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 795) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540243733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540243733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000540243733 none CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 11, 21, 21, 21, 21, 21, 21, 21, 21, 3, 11, 11, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 9, 9, 8, 9, 9, 8, 25, 25, 25, 21, 21, 21, 21, 11, 11, 11, 3, 8, 9, 9, 8, 9, 9, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540243733 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540243733 Building ZINC000428805028 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428805028 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/796 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c1) `ZINC000428805028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428805028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000428805028 none CCC[C@@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 28, 29, 29, 20, 20, 20, 20, 13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 28, 20, 20, 13, 13, 13, 4, 8, 8, 13] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/797 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/797' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c1) `ZINC000428805028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428805028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000428805028 none CCC[C@@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 21, 21, 21, 21, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 21, 21, 14, 14, 14, 4, 8, 8, 14] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000428805028 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028 Building ZINC000428805028 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428805028 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 796) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/796: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c1) `ZINC000428805028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428805028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000428805028 none CCC[C@@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 28, 29, 29, 20, 20, 20, 20, 13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 28, 20, 20, 13, 13, 13, 4, 8, 8, 13] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 797) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c1) `ZINC000428805028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428805028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000428805028 none CCC[C@@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 21, 21, 21, 21, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 21, 21, 14, 14, 14, 4, 8, 8, 14] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000428805028 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805028 Building ZINC000428805029 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428805029 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/798 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c1) `ZINC000428805029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428805029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000428805029 none CCC[C@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 21, 21, 21, 21, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 21, 21, 14, 14, 14, 4, 9, 9, 14] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/799 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/799' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c1) `ZINC000428805029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428805029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000428805029 none CCC[C@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 27, 26, 27, 27, 16, 16, 16, 16, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 11, 29, 29, 29, 29, 29, 29, 29, 27, 27, 27, 26, 16, 16, 11, 11, 11, 4, 7, 7, 11] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000428805029 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029 Building ZINC000428805029 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428805029 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 798) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c1) `ZINC000428805029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428805029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000428805029 none CCC[C@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 21, 21, 21, 21, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 21, 21, 14, 14, 14, 4, 9, 9, 14] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 799) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/799: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c1) `ZINC000428805029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428805029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000428805029 none CCC[C@H](C)NS(=O)(=O)Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 27, 26, 27, 27, 16, 16, 16, 16, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 11, 29, 29, 29, 29, 29, 29, 29, 27, 27, 27, 26, 16, 16, 11, 11, 11, 4, 7, 7, 11] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000428805029 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428805029 Building ZINC000506171987 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506171987 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/800 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)nc1c1ccccc1) `ZINC000506171987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506171987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000506171987 none CCOC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 25, 25, 4, 25, 4, 4, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 4, 4, 4, 12, 12, 4, 12, 12, 36, 36, 36, 36, 36, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 12, 12, 4, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/801 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/801' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)nc1c1ccccc1) `ZINC000506171987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506171987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000506171987 none CCOC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 25, 25, 4, 25, 4, 4, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 4, 4, 4, 12, 12, 4, 12, 12, 36, 36, 36, 36, 36, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 12, 12, 8, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000506171987 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987 Building ZINC000506171987 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506171987 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 800) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/800: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)nc1c1ccccc1) `ZINC000506171987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506171987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000506171987 none CCOC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 25, 25, 4, 25, 4, 4, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 4, 4, 4, 12, 12, 4, 12, 12, 36, 36, 36, 36, 36, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 12, 12, 4, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 801) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/801: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)nc1c1ccccc1) `ZINC000506171987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506171987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000506171987 none CCOC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 25, 25, 4, 25, 4, 4, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 4, 4, 4, 12, 12, 4, 12, 12, 36, 36, 36, 36, 36, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 12, 12, 8, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000506171987 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000506171987 Building ZINC000428808225 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428808225 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/802 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](c1cccc(Br)c1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428808225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428808225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000428808225 none COC(=O)[C@@H](c1cccc(Br)c1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 17, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 12, 16, 5, 12, 12, 28, 28, 26, 28, 28, 28, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 16, 16, 16, 28, 28, 26, 28, 5, 5, 5, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 95 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/803 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/803' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](c1cccc(Br)c1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428808225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428808225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000428808225 none COC(=O)[C@@H](c1cccc(Br)c1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 17, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 10, 17, 4, 10, 10, 30, 30, 26, 30, 30, 30, 2, 4, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 17, 17, 17, 30, 30, 27, 30, 4, 4, 4, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000428808225 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225 Building ZINC000428808225 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428808225 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 802) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/802: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](c1cccc(Br)c1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428808225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428808225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000428808225 none COC(=O)[C@@H](c1cccc(Br)c1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 17, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 12, 16, 5, 12, 12, 28, 28, 26, 28, 28, 28, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 16, 16, 16, 28, 28, 26, 28, 5, 5, 5, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 95 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 803) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/803: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](c1cccc(Br)c1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428808225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428808225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000428808225 none COC(=O)[C@@H](c1cccc(Br)c1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 17, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 10, 17, 4, 10, 10, 30, 30, 26, 30, 30, 30, 2, 4, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 17, 17, 17, 30, 30, 27, 30, 4, 4, 4, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000428808225 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808225 Building ZINC000428808226 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428808226 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/804 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](c1cccc(Br)c1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428808226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428808226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000428808226 none COC(=O)[C@H](c1cccc(Br)c1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 17, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 10, 17, 4, 10, 10, 30, 30, 26, 30, 30, 30, 2, 4, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 17, 17, 17, 30, 30, 30, 30, 4, 4, 4, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/805 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/805' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](c1cccc(Br)c1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428808226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428808226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000428808226 none COC(=O)[C@H](c1cccc(Br)c1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 17, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 12, 17, 5, 12, 12, 29, 29, 27, 29, 29, 29, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 17, 17, 17, 29, 29, 29, 29, 5, 5, 5, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 104 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000428808226 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226 Building ZINC000428808226 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428808226 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 804) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/804: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](c1cccc(Br)c1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428808226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428808226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000428808226 none COC(=O)[C@H](c1cccc(Br)c1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 17, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 10, 17, 4, 10, 10, 30, 30, 26, 30, 30, 30, 2, 4, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 17, 17, 17, 30, 30, 30, 30, 4, 4, 4, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 805) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/805: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](c1cccc(Br)c1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428808226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428808226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000428808226 none COC(=O)[C@H](c1cccc(Br)c1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 17, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 12, 17, 5, 12, 12, 29, 29, 27, 29, 29, 29, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 17, 17, 17, 29, 29, 29, 29, 5, 5, 5, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 104 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000428808226 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000428808226 Building ZINC000540614963 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540614963 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/806 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1C(=O)NC2) `ZINC000540614963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540614963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000540614963 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1C(=O)NC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 20, 20, 4, 20, 20, 20, 20, 20, 20, 4, 4, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 20, 20, 4, 20, 4, 4, 4, 5, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 61 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/807 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/807' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc2c1C(=O)NC2) `ZINC000540614963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540614963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000540614963 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc2c1C(=O)NC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 21, 21, 4, 21, 4, 4, 4, 5, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 65 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540614963 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963 Building ZINC000540614963 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540614963 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 806) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/806: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1C(=O)NC2) `ZINC000540614963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540614963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000540614963 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1C(=O)NC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 20, 20, 4, 20, 20, 20, 20, 20, 20, 4, 4, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 20, 20, 4, 20, 4, 4, 4, 5, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 61 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 807) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/807: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc2c1C(=O)NC2) `ZINC000540614963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540614963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000540614963 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc2c1C(=O)NC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 21, 21, 4, 21, 4, 4, 4, 5, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 65 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540614963 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540614963 Building ZINC000463550481 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000463550481 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/808 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2cccc(Cl)c2)c(F)c1) `ZINC000463550481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000463550481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000463550481 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2cccc(Cl)c2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 16, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 16, 16, 16, 49, 49, 49, 49, 49, 49, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 16, 49, 49, 49, 49, 9] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/809 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/809' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2cccc(Cl)c2)c(F)c1) `ZINC000463550481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000463550481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000463550481 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2cccc(Cl)c2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 16, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 15, 15, 15, 50, 50, 50, 50, 50, 50, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 15, 50, 50, 50, 50, 8] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000463550481 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481 Building ZINC000463550481 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000463550481 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 808) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/808: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2cccc(Cl)c2)c(F)c1) `ZINC000463550481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000463550481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000463550481 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2cccc(Cl)c2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 16, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 16, 16, 16, 49, 49, 49, 49, 49, 49, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 16, 49, 49, 49, 49, 9] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 809) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/809: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2cccc(Cl)c2)c(F)c1) `ZINC000463550481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000463550481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000463550481 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2cccc(Cl)c2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 16, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 15, 15, 15, 50, 50, 50, 50, 50, 50, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 15, 50, 50, 50, 50, 8] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000463550481 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463550481 Building ZINC000540846539 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540846539 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/810 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CCCO)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000540846539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540846539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000540846539 none CCCCN(CCCO)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 5, 12, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 6, 2, 1, 2, 5, 6, 6, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 5, 5, 6, 6, 6, 6, 18, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 150 rigid atoms, others: [4, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 87 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/811 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/811' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CCCO)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000540846539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540846539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000540846539 none CCCCN(CCCO)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 5, 12, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 6, 2, 1, 2, 5, 6, 6, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 5, 5, 6, 6, 6, 6, 18, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 150 rigid atoms, others: [4, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 87 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540846539 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539 Building ZINC000540846539 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540846539 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 810) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CCCO)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000540846539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540846539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000540846539 none CCCCN(CCCO)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 5, 12, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 6, 2, 1, 2, 5, 6, 6, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 5, 5, 6, 6, 6, 6, 18, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 150 rigid atoms, others: [4, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 87 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 811) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CCCO)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000540846539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540846539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000540846539 none CCCCN(CCCO)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 5, 12, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 6, 2, 1, 2, 5, 6, 6, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 5, 5, 6, 6, 6, 6, 18, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 150 rigid atoms, others: [4, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 87 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540846539 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540846539 Building ZINC000609118790 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000609118790 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/812 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1sc2ccccc2c1CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000609118790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000609118790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000609118790 none COC(=O)c1sc2ccccc2c1CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 16, 36, 16, 16, 16, 16, 16, 16, 16, 16, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 36, 36, 36, 16, 16, 16, 16, 9, 9, 2, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/813 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/813' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1sc2ccccc2c1CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000609118790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000609118790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000609118790 none COC(=O)c1sc2ccccc2c1CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 16, 37, 16, 16, 16, 16, 16, 16, 16, 16, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 37, 37, 37, 16, 16, 16, 16, 9, 9, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000609118790 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790 Building ZINC000609118790 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000609118790 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 812) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/812: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1sc2ccccc2c1CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000609118790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000609118790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000609118790 none COC(=O)c1sc2ccccc2c1CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 16, 36, 16, 16, 16, 16, 16, 16, 16, 16, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 36, 36, 36, 16, 16, 16, 16, 9, 9, 2, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 813) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/813: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1sc2ccccc2c1CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000609118790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000609118790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000609118790 none COC(=O)c1sc2ccccc2c1CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 16, 37, 16, 16, 16, 16, 16, 16, 16, 16, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 37, 37, 37, 16, 16, 16, 16, 9, 9, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000609118790 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000609118790 Building ZINC000540892290 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000540892290 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/814 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540892290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892290 none O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 12, 12, 12, 12, 12, 33, 33, 23, 33, 33, 33, 33, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 12, 12, 33, 33, 33, 12, 12, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/815 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/815' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540892290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892290 none O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 33, 33, 25, 33, 33, 33, 33, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 13, 13, 13, 13, 33, 33, 33, 13, 13, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/816 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/816' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892290.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000540892290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892290 none O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 12, 12, 12, 12, 12, 33, 33, 23, 33, 33, 33, 33, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 12, 12, 33, 33, 33, 12, 12, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/817 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/817' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892290.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000540892290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892290 none O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 33, 33, 25, 33, 33, 33, 33, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 13, 13, 13, 13, 33, 33, 33, 13, 13, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540892290 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 Building ZINC000540892290 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000540892290 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 814) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/814: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540892290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892290 none O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 12, 12, 12, 12, 12, 33, 33, 23, 33, 33, 33, 33, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 12, 12, 33, 33, 33, 12, 12, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 815) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/815: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540892290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892290 none O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 33, 33, 25, 33, 33, 33, 33, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 13, 13, 13, 13, 33, 33, 33, 13, 13, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 816) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/816: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892290.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000540892290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892290 none O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 12, 12, 12, 12, 12, 33, 33, 23, 33, 33, 33, 33, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 12, 12, 33, 33, 33, 12, 12, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 817) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/817: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892290.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000540892290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892290 none O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 33, 33, 25, 33, 33, 33, 33, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 13, 13, 13, 13, 33, 33, 33, 13, 13, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540892290 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 Building ZINC000540892290 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000540892290 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 814) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/814: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540892290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892290 none O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 12, 12, 12, 12, 12, 33, 33, 23, 33, 33, 33, 33, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 12, 12, 33, 33, 33, 12, 12, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 815) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/815: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540892290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892290 none O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 33, 33, 25, 33, 33, 33, 33, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 13, 13, 13, 13, 33, 33, 33, 13, 13, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 816) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/816: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892290.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000540892290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892290 none O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 12, 12, 12, 12, 12, 33, 33, 23, 33, 33, 33, 33, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 12, 12, 33, 33, 33, 12, 12, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 817) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/817: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892290.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000540892290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892290 none O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 33, 33, 25, 33, 33, 33, 33, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 13, 13, 13, 13, 33, 33, 33, 13, 13, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540892290 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 Building ZINC000540892290 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000540892290 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 814) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/814: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540892290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892290 none O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 12, 12, 12, 12, 12, 33, 33, 23, 33, 33, 33, 33, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 12, 12, 33, 33, 33, 12, 12, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 815) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/815: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540892290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892290 none O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 33, 33, 25, 33, 33, 33, 33, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 13, 13, 13, 13, 33, 33, 33, 13, 13, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 816) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/816: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892290.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000540892290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892290 none O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 12, 12, 12, 12, 12, 33, 33, 23, 33, 33, 33, 33, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 12, 12, 33, 33, 33, 12, 12, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 817) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/817: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892290.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000540892290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892290 none O=C(N[C@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 33, 33, 25, 33, 33, 33, 33, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 13, 13, 13, 13, 33, 33, 33, 13, 13, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540892290 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892290 Building ZINC000540892293 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000540892293 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/818 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540892293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892293 none O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 33, 33, 26, 33, 33, 33, 33, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 13, 13, 13, 13, 33, 33, 33, 13, 13, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/819 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540892293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892293 none O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 32, 32, 23, 32, 32, 32, 32, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 13, 13, 13, 13, 32, 32, 32, 13, 13, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/820 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/820' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892293.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000540892293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892293 none O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 33, 33, 26, 33, 33, 33, 33, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 13, 13, 13, 13, 33, 33, 33, 13, 13, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/821 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/821' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892293.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000540892293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892293 none O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 32, 32, 23, 32, 32, 32, 32, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 13, 13, 13, 13, 32, 32, 32, 13, 13, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540892293 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 Building ZINC000540892293 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000540892293 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 818) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540892293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892293 none O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 33, 33, 26, 33, 33, 33, 33, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 13, 13, 13, 13, 33, 33, 33, 13, 13, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 819) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540892293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892293 none O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 32, 32, 23, 32, 32, 32, 32, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 13, 13, 13, 13, 32, 32, 32, 13, 13, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 820) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892293.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000540892293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892293 none O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 33, 33, 26, 33, 33, 33, 33, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 13, 13, 13, 13, 33, 33, 33, 13, 13, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 821) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892293.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000540892293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892293 none O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 32, 32, 23, 32, 32, 32, 32, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 13, 13, 13, 13, 32, 32, 32, 13, 13, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540892293 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 Building ZINC000540892293 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000540892293 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 818) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540892293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892293 none O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 33, 33, 26, 33, 33, 33, 33, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 13, 13, 13, 13, 33, 33, 33, 13, 13, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 819) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540892293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892293 none O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 32, 32, 23, 32, 32, 32, 32, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 13, 13, 13, 13, 32, 32, 32, 13, 13, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 820) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892293.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000540892293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892293 none O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 33, 33, 26, 33, 33, 33, 33, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 13, 13, 13, 13, 33, 33, 33, 13, 13, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 821) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892293.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000540892293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892293 none O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 32, 32, 23, 32, 32, 32, 32, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 13, 13, 13, 13, 32, 32, 32, 13, 13, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540892293 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 Building ZINC000540892293 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000540892293 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 818) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540892293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892293 none O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 33, 33, 26, 33, 33, 33, 33, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 13, 13, 13, 13, 33, 33, 33, 13, 13, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 819) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540892293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892293 none O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 32, 32, 23, 32, 32, 32, 32, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 13, 13, 13, 13, 32, 32, 32, 13, 13, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 820) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892293.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000540892293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892293 none O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 33, 33, 26, 33, 33, 33, 33, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 13, 13, 13, 13, 33, 33, 33, 13, 13, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 821) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000540892293.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000540892293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000540892293 none O=C(N[C@@H]1CCN(c2ccc(Cl)c(Cl)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 13, 13, 13, 13, 13, 32, 32, 23, 32, 32, 32, 32, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 13, 13, 13, 13, 32, 32, 32, 13, 13, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540892293 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540892293 Building ZINC000540900076 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540900076 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/822 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)C1CCCCC1) `ZINC000540900076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540900076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000540900076 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 7, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 10, 10, 30, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 127 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/823 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)C1CCCCC1) `ZINC000540900076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540900076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000540900076 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 11, 8, 12, 12, 12, 12, 12, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 11, 11, 33, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 119 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540900076 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076 Building ZINC000540900076 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540900076 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 822) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/822: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)C1CCCCC1) `ZINC000540900076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540900076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000540900076 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 7, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 10, 10, 30, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 127 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 823) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/823: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)C1CCCCC1) `ZINC000540900076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540900076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000540900076 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 11, 8, 12, 12, 12, 12, 12, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 11, 11, 33, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 119 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540900076 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900076 Building ZINC000540900077 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540900077 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/824 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)C1CCCCC1) `ZINC000540900077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540900077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000540900077 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 9, 11, 11, 11, 11, 11, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 10, 10, 30, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/825 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/825' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)C1CCCCC1) `ZINC000540900077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540900077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000540900077 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 7, 11, 11, 11, 11, 11, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 10, 10, 30, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 123 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540900077 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077 Building ZINC000540900077 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540900077 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 824) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/824: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)C1CCCCC1) `ZINC000540900077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540900077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000540900077 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 9, 11, 11, 11, 11, 11, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 10, 10, 30, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 825) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/825: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)C1CCCCC1) `ZINC000540900077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540900077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000540900077 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 7, 11, 11, 11, 11, 11, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 10, 10, 30, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 123 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540900077 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900077 Building ZINC000540900101 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540900101 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/826 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccccc1C) `ZINC000540900101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540900101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000540900101 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 18, 18, 4, 18, 18, 18, 18, 18, 18, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 10, 6, 8, 8, 6, 8, 8, 8, 4, 4, 4, 18, 18, 8, 18, 4, 4, 4, 3, 10, 10, 30, 8, 8, 6, 8, 8, 8, 8] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/827 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/827' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccccc1C) `ZINC000540900101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540900101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000540900101 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 6, 6, 6, 8, 8, 10, 8, 10, 10, 8, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 6, 10, 10, 30, 10, 10, 8, 10, 10, 10, 10] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 107 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540900101 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101 Building ZINC000540900101 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540900101 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 826) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/826: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccccc1C) `ZINC000540900101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540900101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000540900101 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 18, 18, 4, 18, 18, 18, 18, 18, 18, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 10, 6, 8, 8, 6, 8, 8, 8, 4, 4, 4, 18, 18, 8, 18, 4, 4, 4, 3, 10, 10, 30, 8, 8, 6, 8, 8, 8, 8] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 827) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/827: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccccc1C) `ZINC000540900101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540900101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000540900101 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 6, 6, 6, 8, 8, 10, 8, 10, 10, 8, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 6, 10, 10, 30, 10, 10, 8, 10, 10, 10, 10] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 107 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540900101 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900101 Building ZINC000540900105 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540900105 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/828 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccccc1C) `ZINC000540900105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540900105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000540900105 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 6, 6, 6, 8, 8, 11, 8, 10, 10, 8, 10, 10, 10, 3, 3, 3, 13, 13, 4, 13, 3, 3, 3, 6, 11, 11, 33, 10, 10, 8, 10, 10, 10, 10] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 117 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/829 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/829' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccccc1C) `ZINC000540900105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540900105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000540900105 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 18, 18, 4, 18, 18, 18, 18, 18, 18, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 10, 6, 8, 8, 6, 8, 8, 8, 4, 4, 4, 18, 18, 4, 18, 4, 4, 4, 3, 10, 10, 30, 8, 8, 6, 8, 8, 8, 8] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 127 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540900105 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105 Building ZINC000540900105 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000540900105 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 828) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccccc1C) `ZINC000540900105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000540900105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000540900105 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 6, 6, 6, 8, 8, 11, 8, 10, 10, 8, 10, 10, 10, 3, 3, 3, 13, 13, 4, 13, 3, 3, 3, 6, 11, 11, 33, 10, 10, 8, 10, 10, 10, 10] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 117 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 829) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccccc1C) `ZINC000540900105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000540900105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000540900105 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 18, 18, 4, 18, 18, 18, 18, 18, 18, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 10, 6, 8, 8, 6, 8, 8, 8, 4, 4, 4, 18, 18, 4, 18, 4, 4, 4, 3, 10, 10, 30, 8, 8, 6, 8, 8, 8, 8] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 127 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000540900105 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000540900105 Building ZINC000541007510 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541007510 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/830 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccc(F)cc1)c1cccc(S(C)(=O)=O)c1) `ZINC000541007510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541007510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000541007510 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccc(F)cc1)c1cccc(S(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 8, 8, 16, 16, 16, 16, 16, 16, 8, 37, 37, 15, 37, 37, 48, 48, 48, 37, 2, 2, 2, 2, 2, 2, 4, 16, 16, 16, 16, 37, 37, 19, 48, 48, 48, 37] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 202 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/831 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccc(F)cc1)c1cccc(S(C)(=O)=O)c1) `ZINC000541007510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541007510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000541007510 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccc(F)cc1)c1cccc(S(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 8, 8, 12, 12, 8, 8, 12, 12, 8, 35, 35, 17, 35, 35, 46, 46, 46, 35, 2, 2, 2, 2, 2, 2, 4, 12, 12, 12, 12, 35, 35, 18, 46, 46, 46, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541007510 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510 Building ZINC000541007510 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541007510 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 830) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/830: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccc(F)cc1)c1cccc(S(C)(=O)=O)c1) `ZINC000541007510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541007510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000541007510 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccc(F)cc1)c1cccc(S(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 8, 8, 16, 16, 16, 16, 16, 16, 8, 37, 37, 15, 37, 37, 48, 48, 48, 37, 2, 2, 2, 2, 2, 2, 4, 16, 16, 16, 16, 37, 37, 19, 48, 48, 48, 37] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 202 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 831) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/831: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccc(F)cc1)c1cccc(S(C)(=O)=O)c1) `ZINC000541007510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541007510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000541007510 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccc(F)cc1)c1cccc(S(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 8, 8, 12, 12, 8, 8, 12, 12, 8, 35, 35, 17, 35, 35, 46, 46, 46, 35, 2, 2, 2, 2, 2, 2, 4, 12, 12, 12, 12, 35, 35, 18, 46, 46, 46, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541007510 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007510 Building ZINC000541007511 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541007511 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/832 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccc(F)cc1)c1cccc(S(C)(=O)=O)c1) `ZINC000541007511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541007511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000541007511 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccc(F)cc1)c1cccc(S(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 8, 8, 12, 12, 8, 8, 12, 12, 8, 35, 35, 15, 35, 35, 46, 46, 46, 35, 2, 2, 2, 2, 2, 2, 4, 12, 12, 12, 12, 35, 35, 18, 46, 46, 46, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 196 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/833 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/833' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccc(F)cc1)c1cccc(S(C)(=O)=O)c1) `ZINC000541007511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541007511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000541007511 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccc(F)cc1)c1cccc(S(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 8, 8, 15, 15, 15, 15, 15, 15, 8, 37, 37, 17, 37, 37, 48, 48, 48, 37, 2, 2, 2, 2, 2, 2, 4, 15, 15, 15, 15, 37, 37, 19, 48, 48, 48, 37] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541007511 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511 Building ZINC000541007511 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541007511 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 832) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccc(F)cc1)c1cccc(S(C)(=O)=O)c1) `ZINC000541007511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541007511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000541007511 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccc(F)cc1)c1cccc(S(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 8, 8, 12, 12, 8, 8, 12, 12, 8, 35, 35, 15, 35, 35, 46, 46, 46, 35, 2, 2, 2, 2, 2, 2, 4, 12, 12, 12, 12, 35, 35, 18, 46, 46, 46, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 196 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 833) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccc(F)cc1)c1cccc(S(C)(=O)=O)c1) `ZINC000541007511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541007511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000541007511 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccc(F)cc1)c1cccc(S(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 8, 8, 15, 15, 15, 15, 15, 15, 8, 37, 37, 17, 37, 37, 48, 48, 48, 37, 2, 2, 2, 2, 2, 2, 4, 15, 15, 15, 15, 37, 37, 19, 48, 48, 48, 37] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541007511 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541007511 Building ZINC000541009610 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541009610 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/834 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(Cc2cccc(C(F)(F)F)c2)C1=O) `ZINC000541009610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541009610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000541009610 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(Cc2cccc(C(F)(F)F)c2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 8, 12, 12, 12, 12, 12, 12, 27, 50, 50, 41, 50, 50, 50, 50, 50, 50, 12, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 12, 12, 12, 27, 27, 50, 50, 41, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/835 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(Cc2cccc(C(F)(F)F)c2)C1=O) `ZINC000541009610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541009610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000541009610 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(Cc2cccc(C(F)(F)F)c2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 7, 12, 12, 12, 12, 12, 12, 27, 50, 50, 40, 50, 50, 50, 50, 50, 50, 12, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 12, 12, 12, 27, 27, 50, 50, 45, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541009610 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610 Building ZINC000541009610 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541009610 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 834) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/834: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(Cc2cccc(C(F)(F)F)c2)C1=O) `ZINC000541009610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541009610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000541009610 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(Cc2cccc(C(F)(F)F)c2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 8, 12, 12, 12, 12, 12, 12, 27, 50, 50, 41, 50, 50, 50, 50, 50, 50, 12, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 12, 12, 12, 27, 27, 50, 50, 41, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 835) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/835: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(Cc2cccc(C(F)(F)F)c2)C1=O) `ZINC000541009610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541009610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000541009610 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(Cc2cccc(C(F)(F)F)c2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 7, 12, 12, 12, 12, 12, 12, 27, 50, 50, 40, 50, 50, 50, 50, 50, 50, 12, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 12, 12, 12, 27, 27, 50, 50, 45, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541009610 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009610 Building ZINC000541009611 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541009611 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/836 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(Cc2cccc(C(F)(F)F)c2)C1=O) `ZINC000541009611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541009611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000541009611 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(Cc2cccc(C(F)(F)F)c2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 9, 13, 13, 13, 13, 13, 13, 28, 50, 50, 41, 50, 50, 50, 50, 50, 50, 13, 13, 2, 2, 2, 2, 2, 2, 3, 13, 13, 13, 13, 13, 13, 28, 28, 50, 50, 41, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/837 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(Cc2cccc(C(F)(F)F)c2)C1=O) `ZINC000541009611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541009611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000541009611 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(Cc2cccc(C(F)(F)F)c2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 8, 11, 11, 11, 11, 11, 11, 26, 50, 50, 39, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 11, 11, 26, 26, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541009611 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611 Building ZINC000541009611 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541009611 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 836) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/836: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(Cc2cccc(C(F)(F)F)c2)C1=O) `ZINC000541009611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541009611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000541009611 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(Cc2cccc(C(F)(F)F)c2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 9, 13, 13, 13, 13, 13, 13, 28, 50, 50, 41, 50, 50, 50, 50, 50, 50, 13, 13, 2, 2, 2, 2, 2, 2, 3, 13, 13, 13, 13, 13, 13, 28, 28, 50, 50, 41, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 837) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/837: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(Cc2cccc(C(F)(F)F)c2)C1=O) `ZINC000541009611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541009611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000541009611 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(Cc2cccc(C(F)(F)F)c2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 8, 11, 11, 11, 11, 11, 11, 26, 50, 50, 39, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 11, 11, 26, 26, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541009611 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541009611 Building ZINC000463861193 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000463861193 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/838 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCCOc1ccccc1)C1CCOCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000463861193.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000463861193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000463861193 none O=C(N(CCCOc1ccccc1)C1CCOCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 5, 7, 12, 32, 33, 33, 32, 33, 33, 3, 4, 4, 4, 4, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 7, 7, 12, 12, 33, 33, 32, 33, 33, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/839 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCCOc1ccccc1)C1CCOCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000463861193.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000463861193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000463861193 none O=C(N(CCCOc1ccccc1)C1CCOCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 4, 6, 10, 29, 30, 30, 29, 30, 30, 2, 3, 3, 3, 3, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 6, 6, 10, 10, 30, 30, 29, 30, 30, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 19, 20, 21] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 88 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000463861193 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193 Building ZINC000463861193 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000463861193 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 838) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/838: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCCOc1ccccc1)C1CCOCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000463861193.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000463861193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000463861193 none O=C(N(CCCOc1ccccc1)C1CCOCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 5, 7, 12, 32, 33, 33, 32, 33, 33, 3, 4, 4, 4, 4, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 7, 7, 12, 12, 33, 33, 32, 33, 33, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 839) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/839: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCCOc1ccccc1)C1CCOCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000463861193.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000463861193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000463861193 none O=C(N(CCCOc1ccccc1)C1CCOCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 4, 6, 10, 29, 30, 30, 29, 30, 30, 2, 3, 3, 3, 3, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 6, 6, 10, 10, 30, 30, 29, 30, 30, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 19, 20, 21] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 88 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000463861193 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000463861193 Building ZINC000507855292 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000507855292 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/840 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@@](C)CC1) `ZINC000507855292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000507855292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000507855292 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/841 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@@](C)CC1) `ZINC000507855292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000507855292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000507855292 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/842 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/842' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@](C)CC1) `ZINC000507855292.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000507855292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000507855292 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/843 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/843' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@](C)CC1) `ZINC000507855292.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000507855292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000507855292 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 5, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000507855292 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 Building ZINC000507855292 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000507855292 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 840) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/840: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@@](C)CC1) `ZINC000507855292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000507855292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000507855292 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 841) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/841: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@@](C)CC1) `ZINC000507855292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000507855292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000507855292 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 842) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/842: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@](C)CC1) `ZINC000507855292.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000507855292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000507855292 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 843) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/843: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@](C)CC1) `ZINC000507855292.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000507855292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000507855292 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 5, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000507855292 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 Building ZINC000507855292 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000507855292 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 840) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/840: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@@](C)CC1) `ZINC000507855292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000507855292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000507855292 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 841) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/841: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@@](C)CC1) `ZINC000507855292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000507855292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000507855292 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 842) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/842: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@](C)CC1) `ZINC000507855292.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000507855292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000507855292 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 843) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/843: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@](C)CC1) `ZINC000507855292.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000507855292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000507855292 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 5, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000507855292 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 Building ZINC000507855292 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000507855292 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 840) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/840: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@@](C)CC1) `ZINC000507855292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000507855292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000507855292 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 841) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/841: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@@](C)CC1) `ZINC000507855292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000507855292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000507855292 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 842) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/842: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@](C)CC1) `ZINC000507855292.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000507855292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000507855292 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 843) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/843: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@](C)CC1) `ZINC000507855292.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000507855292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000507855292 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 5, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000507855292 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000507855292 Building ZINC000541044903 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541044903 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/844 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(N(C)C)n1) `ZINC000541044903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541044903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000541044903 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(N(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 19, 19, 4, 19, 19, 19, 19, 19, 19, 4, 4, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 10, 10, 6, 4, 4, 4, 19, 19, 4, 19, 4, 4, 4, 4, 6, 6, 6, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 73 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/845 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(N(C)C)n1) `ZINC000541044903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541044903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000541044903 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(N(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 20, 20, 4, 20, 20, 20, 20, 20, 20, 4, 4, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 9, 9, 6, 4, 4, 4, 20, 20, 6, 20, 4, 4, 4, 4, 6, 6, 6, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 77 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541044903 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903 Building ZINC000541044903 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541044903 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 844) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/844: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(N(C)C)n1) `ZINC000541044903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541044903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000541044903 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(N(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 19, 19, 4, 19, 19, 19, 19, 19, 19, 4, 4, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 10, 10, 6, 4, 4, 4, 19, 19, 4, 19, 4, 4, 4, 4, 6, 6, 6, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 73 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 845) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/845: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(N(C)C)n1) `ZINC000541044903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541044903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000541044903 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(N(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 20, 20, 4, 20, 20, 20, 20, 20, 20, 4, 4, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 9, 9, 6, 4, 4, 4, 20, 20, 6, 20, 4, 4, 4, 4, 6, 6, 6, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 77 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541044903 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541044903 Building ZINC000541035797 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541035797 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/846 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCNC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)ccc1Cl) `ZINC000541035797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541035797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000541035797 none CCN(CC)CCNC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 50, 50, 33, 10, 10, 8, 10, 8, 8, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 33, 33, 10, 8, 3, 2, 2, 2, 2, 2, 2, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/847 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/847' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCNC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)ccc1Cl) `ZINC000541035797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541035797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000541035797 none CCN(CC)CCNC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 50, 50, 35, 13, 13, 9, 13, 9, 9, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 35, 35, 13, 9, 3, 2, 2, 2, 2, 2, 2, 9, 9] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541035797 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797 Building ZINC000541035797 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541035797 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 846) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCNC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)ccc1Cl) `ZINC000541035797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541035797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000541035797 none CCN(CC)CCNC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 50, 50, 33, 10, 10, 8, 10, 8, 8, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 33, 33, 10, 8, 3, 2, 2, 2, 2, 2, 2, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 847) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/847: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCNC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)ccc1Cl) `ZINC000541035797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541035797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000541035797 none CCN(CC)CCNC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 50, 50, 35, 13, 13, 9, 13, 9, 9, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 35, 35, 13, 9, 3, 2, 2, 2, 2, 2, 2, 9, 9] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541035797 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541035797 Building ZINC000521464124 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000521464124 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/848 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(NC4CC4)cc32)C1) `ZINC000521464124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000521464124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000521464124 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(NC4CC4)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 6, 16, 16, 21, 21, 21, 21, 21, 21, 21, 21, 21, 50, 50, 50, 21, 21, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 4, 4] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 6, 7, 8, 9, 10, 2, 3, 4, 38, 5, 37] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/849 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/849' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(NC4CC4)cc32)C1) `ZINC000521464124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000521464124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000521464124 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(NC4CC4)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 6, 6, 7, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 50, 50, 50, 17, 17, 6, 2, 2, 2, 2, 2, 2, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 6, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000521464124 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124 Building ZINC000521464124 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000521464124 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 848) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(NC4CC4)cc32)C1) `ZINC000521464124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000521464124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000521464124 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(NC4CC4)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 6, 16, 16, 21, 21, 21, 21, 21, 21, 21, 21, 21, 50, 50, 50, 21, 21, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 4, 4] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 6, 7, 8, 9, 10, 2, 3, 4, 38, 5, 37] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 849) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(NC4CC4)cc32)C1) `ZINC000521464124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000521464124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000521464124 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(NC4CC4)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 6, 6, 7, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 50, 50, 50, 17, 17, 6, 2, 2, 2, 2, 2, 2, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 6, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000521464124 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000521464124 Building ZINC000508290422 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000508290422 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/850 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@@H]1C) `ZINC000508290422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000508290422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000508290422 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 13, 19, 34, 34, 39, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 13, 13, 13, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/851 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/851' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@@H]1C) `ZINC000508290422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000508290422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000508290422 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 12, 19, 31, 31, 40, 40, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 12, 12, 12, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000508290422 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422 Building ZINC000508290422 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000508290422 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 850) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/850: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@@H]1C) `ZINC000508290422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000508290422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000508290422 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 13, 19, 34, 34, 39, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 13, 13, 13, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 851) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@@H]1C) `ZINC000508290422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000508290422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000508290422 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 12, 19, 31, 31, 40, 40, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 12, 12, 12, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000508290422 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290422 Building ZINC000508290423 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000508290423 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/852 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@H]1C) `ZINC000508290423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000508290423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000508290423 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 20, 36, 36, 37, 37, 37, 37, 37, 37, 37, 37, 37, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 10, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/853 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/853' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@H]1C) `ZINC000508290423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000508290423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000508290423 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 11, 21, 35, 35, 40, 40, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 11, 11, 11, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 98 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000508290423 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423 Building ZINC000508290423 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000508290423 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 852) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@H]1C) `ZINC000508290423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000508290423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000508290423 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 20, 36, 36, 37, 37, 37, 37, 37, 37, 37, 37, 37, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 10, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 853) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@H]1C) `ZINC000508290423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000508290423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000508290423 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 11, 21, 35, 35, 40, 40, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 11, 11, 11, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 98 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000508290423 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290423 Building ZINC000508290424 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000508290424 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/854 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@@H](C)CCC[C@@H]1C) `ZINC000508290424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000508290424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000508290424 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@@H](C)CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 20, 40, 40, 41, 41, 41, 41, 41, 41, 41, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 10, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/855 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/855' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@@H](C)CCC[C@@H]1C) `ZINC000508290424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000508290424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000508290424 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@@H](C)CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 12, 18, 33, 33, 39, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 12, 12, 12, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000508290424 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424 Building ZINC000508290424 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000508290424 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 854) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/854: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@@H](C)CCC[C@@H]1C) `ZINC000508290424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000508290424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000508290424 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@@H](C)CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 20, 40, 40, 41, 41, 41, 41, 41, 41, 41, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 10, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 855) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@@H](C)CCC[C@@H]1C) `ZINC000508290424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000508290424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000508290424 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@@H](C)CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 12, 18, 33, 33, 39, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 12, 12, 12, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000508290424 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000508290424 Building ZINC000464109494 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464109494 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/856 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(S(C)(=O)=O)c2)c2ccc(F)c(F)c2)cc1) `ZINC000464109494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464109494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000464109494 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(S(C)(=O)=O)c2)c2ccc(F)c(F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 15, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 23, 23, 10, 23, 23, 26, 26, 26, 23, 6, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 3, 23, 23, 12, 26, 26, 26, 23, 19, 19, 19, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 110 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/857 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/857' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(S(C)(=O)=O)c2)c2ccc(F)c(F)c2)cc1) `ZINC000464109494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464109494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000464109494 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(S(C)(=O)=O)c2)c2ccc(F)c(F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 15, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 21, 21, 9, 21, 21, 26, 26, 26, 21, 5, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 2, 2, 2, 2, 3, 21, 21, 11, 26, 26, 26, 21, 20, 20, 20, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 117 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464109494 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494 Building ZINC000464109494 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464109494 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 856) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(S(C)(=O)=O)c2)c2ccc(F)c(F)c2)cc1) `ZINC000464109494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464109494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000464109494 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(S(C)(=O)=O)c2)c2ccc(F)c(F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 15, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 23, 23, 10, 23, 23, 26, 26, 26, 23, 6, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 3, 23, 23, 12, 26, 26, 26, 23, 19, 19, 19, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 110 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 857) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(S(C)(=O)=O)c2)c2ccc(F)c(F)c2)cc1) `ZINC000464109494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464109494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000464109494 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(S(C)(=O)=O)c2)c2ccc(F)c(F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 15, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 21, 21, 9, 21, 21, 26, 26, 26, 21, 5, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 2, 2, 2, 2, 3, 21, 21, 11, 26, 26, 26, 21, 20, 20, 20, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 117 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464109494 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109494 Building ZINC000464109500 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464109500 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/858 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2cccc(S(C)(=O)=O)c2)c2ccc(F)c(F)c2)cc1) `ZINC000464109500.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464109500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000464109500 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2cccc(S(C)(=O)=O)c2)c2ccc(F)c(F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 15, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 20, 20, 9, 20, 20, 25, 25, 25, 20, 5, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 2, 2, 2, 2, 3, 20, 20, 12, 25, 25, 25, 20, 20, 20, 20, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 125 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/859 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/859' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2cccc(S(C)(=O)=O)c2)c2ccc(F)c(F)c2)cc1) `ZINC000464109500.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464109500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000464109500 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2cccc(S(C)(=O)=O)c2)c2ccc(F)c(F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 15, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 23, 23, 10, 23, 23, 26, 26, 26, 23, 6, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 3, 23, 23, 12, 26, 26, 26, 23, 19, 19, 19, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 110 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464109500 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500 Building ZINC000464109500 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464109500 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 858) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/858: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2cccc(S(C)(=O)=O)c2)c2ccc(F)c(F)c2)cc1) `ZINC000464109500.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464109500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000464109500 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2cccc(S(C)(=O)=O)c2)c2ccc(F)c(F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 15, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 20, 20, 9, 20, 20, 25, 25, 25, 20, 5, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 2, 2, 2, 2, 3, 20, 20, 12, 25, 25, 25, 20, 20, 20, 20, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 125 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 859) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/859: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2cccc(S(C)(=O)=O)c2)c2ccc(F)c(F)c2)cc1) `ZINC000464109500.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464109500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000464109500 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2cccc(S(C)(=O)=O)c2)c2ccc(F)c(F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 15, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 23, 23, 10, 23, 23, 26, 26, 26, 23, 6, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 3, 23, 23, 12, 26, 26, 26, 23, 19, 19, 19, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 110 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464109500 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464109500 Building ZINC000464114600 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464114600 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/860 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cc2nnc3n2CCCCC3)cc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000464114600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464114600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000464114600 none O=C(Nc1ccc(Cc2nnc3n2CCCCC3)cc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 18, 18, 32, 32, 18, 32, 32, 32, 32, 32, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 18, 18, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/861 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/861' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cc2nnc3n2CCCCC3)cc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000464114600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464114600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000464114600 none O=C(Nc1ccc(Cc2nnc3n2CCCCC3)cc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 4, 17, 17, 31, 31, 17, 31, 31, 31, 31, 31, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 17, 17, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464114600 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600 Building ZINC000464114600 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464114600 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 860) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cc2nnc3n2CCCCC3)cc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000464114600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464114600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000464114600 none O=C(Nc1ccc(Cc2nnc3n2CCCCC3)cc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 18, 18, 32, 32, 18, 32, 32, 32, 32, 32, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 18, 18, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 861) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cc2nnc3n2CCCCC3)cc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000464114600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464114600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000464114600 none O=C(Nc1ccc(Cc2nnc3n2CCCCC3)cc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 4, 17, 17, 31, 31, 17, 31, 31, 31, 31, 31, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 17, 17, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464114600 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464114600 Building ZINC000541310798 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541310798 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/862 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(Br)ccc1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000541310798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541310798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000541310798 none COc1cc(Br)ccc1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 32, 32, 32, 32, 32, 32, 32, 19, 15, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 38, 38, 38, 32, 32, 32, 19, 19, 19, 19, 14, 14, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/863 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/863' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(Br)ccc1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000541310798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541310798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000541310798 none COc1cc(Br)ccc1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 33, 33, 33, 33, 33, 33, 33, 19, 15, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 38, 38, 38, 33, 33, 33, 19, 19, 19, 19, 14, 14, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541310798 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798 Building ZINC000541310798 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541310798 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 862) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/862: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(Br)ccc1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000541310798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541310798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000541310798 none COc1cc(Br)ccc1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 32, 32, 32, 32, 32, 32, 32, 19, 15, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 38, 38, 38, 32, 32, 32, 19, 19, 19, 19, 14, 14, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 863) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/863: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(Br)ccc1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000541310798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541310798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000541310798 none COc1cc(Br)ccc1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 33, 33, 33, 33, 33, 33, 33, 19, 15, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 38, 38, 38, 33, 33, 33, 19, 19, 19, 19, 14, 14, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541310798 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541310798 Building ZINC000541344823 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541344823 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/864 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2nnnc2C(C)C)c(C)c1) `ZINC000541344823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541344823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000541344823 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2nnnc2C(C)C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 15, 15, 10, 14, 25, 25, 25, 25, 25, 34, 34, 15, 15, 15, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 15, 15, 34, 34, 34, 34, 34, 34, 34, 15, 15, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/865 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/865' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2nnnc2C(C)C)c(C)c1) `ZINC000541344823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541344823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000541344823 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2nnnc2C(C)C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 19, 19, 12, 12, 30, 30, 30, 30, 30, 41, 41, 19, 19, 19, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 19, 19, 41, 41, 41, 41, 41, 41, 41, 19, 19, 19, 19] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541344823 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823 Building ZINC000541344823 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541344823 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 864) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2nnnc2C(C)C)c(C)c1) `ZINC000541344823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541344823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000541344823 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2nnnc2C(C)C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 15, 15, 10, 14, 25, 25, 25, 25, 25, 34, 34, 15, 15, 15, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 15, 15, 34, 34, 34, 34, 34, 34, 34, 15, 15, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 865) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2nnnc2C(C)C)c(C)c1) `ZINC000541344823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541344823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000541344823 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2nnnc2C(C)C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 19, 19, 12, 12, 30, 30, 30, 30, 30, 41, 41, 19, 19, 19, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 19, 19, 41, 41, 41, 41, 41, 41, 41, 19, 19, 19, 19] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541344823 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541344823 Building ZINC000464209738 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464209738 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/866 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl) `ZINC000464209738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464209738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000464209738 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 11, 11, 41, 41, 41, 41, 41, 41, 41, 41, 41, 11, 16, 16, 11, 16, 16, 16, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 41, 41, 41, 41, 41, 41, 41, 16, 16, 12, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 110 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/867 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/867' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl) `ZINC000464209738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464209738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000464209738 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 11, 17, 17, 12, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 39, 39, 39, 39, 39, 39, 39, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 120 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464209738 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738 Building ZINC000464209738 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464209738 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 866) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/866: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl) `ZINC000464209738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464209738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000464209738 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 11, 11, 41, 41, 41, 41, 41, 41, 41, 41, 41, 11, 16, 16, 11, 16, 16, 16, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 41, 41, 41, 41, 41, 41, 41, 16, 16, 12, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 110 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 867) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/867: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl) `ZINC000464209738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464209738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000464209738 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 11, 17, 17, 12, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 39, 39, 39, 39, 39, 39, 39, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 120 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464209738 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209738 Building ZINC000464209742 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464209742 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/868 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl) `ZINC000464209742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464209742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000464209742 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 11, 18, 18, 13, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 39, 39, 39, 39, 39, 39, 39, 18, 18, 13, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 110 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/869 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl) `ZINC000464209742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464209742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000464209742 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 11, 11, 41, 41, 41, 41, 41, 41, 41, 41, 41, 11, 17, 17, 12, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 41, 41, 41, 41, 41, 41, 41, 17, 17, 12, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 109 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464209742 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742 Building ZINC000464209742 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464209742 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 868) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/868: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl) `ZINC000464209742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464209742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000464209742 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 11, 18, 18, 13, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 39, 39, 39, 39, 39, 39, 39, 18, 18, 13, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 110 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 869) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/869: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl) `ZINC000464209742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464209742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000464209742 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 11, 11, 41, 41, 41, 41, 41, 41, 41, 41, 41, 11, 17, 17, 12, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 41, 41, 41, 41, 41, 41, 41, 17, 17, 12, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 109 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464209742 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464209742 Building ZINC000464226771 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464226771 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/870 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccc(F)cc2)c2cccc(S(C)(=O)=O)c2)cc1) `ZINC000464226771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464226771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000464226771 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccc(F)cc2)c2cccc(S(C)(=O)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 8, 14, 14, 8, 8, 14, 14, 8, 37, 37, 16, 37, 37, 47, 47, 47, 37, 3, 3, 3, 3, 3, 3, 3, 4, 14, 14, 14, 14, 37, 37, 16, 47, 47, 47, 37, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 205 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/871 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccc(F)cc2)c2cccc(S(C)(=O)=O)c2)cc1) `ZINC000464226771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464226771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000464226771 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccc(F)cc2)c2cccc(S(C)(=O)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 7, 7, 11, 11, 7, 36, 36, 13, 36, 36, 47, 47, 47, 36, 3, 3, 3, 3, 3, 3, 3, 4, 11, 11, 11, 11, 36, 36, 14, 47, 47, 47, 36, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464226771 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771 Building ZINC000464226771 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464226771 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 870) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/870: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccc(F)cc2)c2cccc(S(C)(=O)=O)c2)cc1) `ZINC000464226771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464226771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000464226771 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccc(F)cc2)c2cccc(S(C)(=O)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 8, 14, 14, 8, 8, 14, 14, 8, 37, 37, 16, 37, 37, 47, 47, 47, 37, 3, 3, 3, 3, 3, 3, 3, 4, 14, 14, 14, 14, 37, 37, 16, 47, 47, 47, 37, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 205 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 871) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/871: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccc(F)cc2)c2cccc(S(C)(=O)=O)c2)cc1) `ZINC000464226771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464226771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000464226771 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccc(F)cc2)c2cccc(S(C)(=O)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 7, 7, 11, 11, 7, 36, 36, 13, 36, 36, 47, 47, 47, 36, 3, 3, 3, 3, 3, 3, 3, 4, 11, 11, 11, 11, 36, 36, 14, 47, 47, 47, 36, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464226771 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226771 Building ZINC000464226772 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464226772 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/872 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccc(F)cc2)c2cccc(S(C)(=O)=O)c2)cc1) `ZINC000464226772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464226772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000464226772 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccc(F)cc2)c2cccc(S(C)(=O)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 7, 7, 11, 11, 7, 37, 37, 13, 37, 37, 47, 47, 47, 37, 3, 3, 3, 3, 3, 3, 3, 4, 11, 11, 11, 11, 37, 37, 14, 47, 47, 47, 37, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/873 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccc(F)cc2)c2cccc(S(C)(=O)=O)c2)cc1) `ZINC000464226772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464226772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000464226772 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccc(F)cc2)c2cccc(S(C)(=O)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 8, 14, 14, 8, 8, 14, 14, 8, 37, 37, 14, 37, 37, 48, 48, 48, 37, 3, 3, 3, 3, 3, 3, 3, 4, 14, 14, 14, 14, 37, 37, 16, 48, 48, 48, 37, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 204 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464226772 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772 Building ZINC000464226772 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464226772 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 872) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/872: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccc(F)cc2)c2cccc(S(C)(=O)=O)c2)cc1) `ZINC000464226772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464226772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000464226772 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccc(F)cc2)c2cccc(S(C)(=O)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 7, 7, 11, 11, 7, 37, 37, 13, 37, 37, 47, 47, 47, 37, 3, 3, 3, 3, 3, 3, 3, 4, 11, 11, 11, 11, 37, 37, 14, 47, 47, 47, 37, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 873) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/873: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccc(F)cc2)c2cccc(S(C)(=O)=O)c2)cc1) `ZINC000464226772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464226772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000464226772 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccc(F)cc2)c2cccc(S(C)(=O)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 8, 14, 14, 8, 8, 14, 14, 8, 37, 37, 14, 37, 37, 48, 48, 48, 37, 3, 3, 3, 3, 3, 3, 3, 4, 14, 14, 14, 14, 37, 37, 16, 48, 48, 48, 37, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 204 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464226772 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464226772 Building ZINC000464222019 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464222019 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/874 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)c1cccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccc(F)cc2)c1) `ZINC000464222019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464222019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000464222019 none CS(=O)(=O)c1cccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 36, 47, 47, 36, 13, 36, 36, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 11, 11, 7, 7, 11, 11, 36, 47, 47, 47, 14, 36, 36, 4, 3, 3, 3, 3, 11, 11, 11, 11, 36] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/875 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/875' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)c1cccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccc(F)cc2)c1) `ZINC000464222019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464222019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000464222019 none CS(=O)(=O)c1cccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 37, 47, 47, 37, 10, 37, 37, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 14, 14, 8, 8, 14, 14, 37, 47, 47, 47, 15, 37, 37, 4, 3, 3, 3, 3, 14, 14, 14, 14, 37] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 207 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464222019 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019 Building ZINC000464222019 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464222019 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 874) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)c1cccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccc(F)cc2)c1) `ZINC000464222019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464222019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000464222019 none CS(=O)(=O)c1cccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 36, 47, 47, 36, 13, 36, 36, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 11, 11, 7, 7, 11, 11, 36, 47, 47, 47, 14, 36, 36, 4, 3, 3, 3, 3, 11, 11, 11, 11, 36] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 875) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)c1cccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccc(F)cc2)c1) `ZINC000464222019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464222019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000464222019 none CS(=O)(=O)c1cccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 37, 47, 47, 37, 10, 37, 37, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 14, 14, 8, 8, 14, 14, 37, 47, 47, 47, 15, 37, 37, 4, 3, 3, 3, 3, 14, 14, 14, 14, 37] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 207 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464222019 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222019 Building ZINC000464222020 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464222020 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/876 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)c1cccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccc(F)cc2)c1) `ZINC000464222020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464222020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000464222020 none CS(=O)(=O)c1cccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 37, 47, 47, 37, 37, 37, 37, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 14, 14, 8, 8, 14, 14, 37, 47, 47, 47, 37, 37, 37, 4, 3, 3, 3, 3, 14, 14, 14, 14, 37] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 158 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/877 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/877' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)c1cccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccc(F)cc2)c1) `ZINC000464222020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464222020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000464222020 none CS(=O)(=O)c1cccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 37, 47, 47, 37, 13, 37, 37, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 7, 11, 11, 7, 7, 11, 11, 37, 47, 47, 47, 14, 37, 37, 4, 3, 3, 3, 3, 11, 11, 11, 11, 37] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 188 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464222020 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020 Building ZINC000464222020 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464222020 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 876) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)c1cccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccc(F)cc2)c1) `ZINC000464222020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464222020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000464222020 none CS(=O)(=O)c1cccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 37, 47, 47, 37, 37, 37, 37, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 14, 14, 8, 8, 14, 14, 37, 47, 47, 47, 37, 37, 37, 4, 3, 3, 3, 3, 14, 14, 14, 14, 37] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 158 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 877) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)c1cccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccc(F)cc2)c1) `ZINC000464222020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464222020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000464222020 none CS(=O)(=O)c1cccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 37, 47, 47, 37, 13, 37, 37, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 7, 11, 11, 7, 7, 11, 11, 37, 47, 47, 47, 14, 37, 37, 4, 3, 3, 3, 3, 11, 11, 11, 11, 37] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 188 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464222020 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464222020 Building ZINC000541412739 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541412739 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/878 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1c1nnnn1C(C)C) `ZINC000541412739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541412739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000541412739 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1c1nnnn1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 13, 26, 26, 26, 26, 26, 31, 31, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 6, 13, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 101 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/879 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/879' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1c1nnnn1C(C)C) `ZINC000541412739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541412739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000541412739 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1c1nnnn1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 12, 25, 25, 25, 25, 25, 31, 31, 3, 3, 3, 10, 10, 4, 10, 10, 3, 3, 3, 6, 12, 12, 12, 12, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 107 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541412739 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739 Building ZINC000541412739 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541412739 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 878) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1c1nnnn1C(C)C) `ZINC000541412739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541412739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000541412739 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1c1nnnn1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 13, 26, 26, 26, 26, 26, 31, 31, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 6, 13, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 101 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 879) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1c1nnnn1C(C)C) `ZINC000541412739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541412739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000541412739 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1c1nnnn1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 12, 25, 25, 25, 25, 25, 31, 31, 3, 3, 3, 10, 10, 4, 10, 10, 3, 3, 3, 6, 12, 12, 12, 12, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 107 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541412739 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541412739 Building ZINC000464278509 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464278509 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/880 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1nccn1Cc1ccccc1) `ZINC000464278509.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464278509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000464278509 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1nccn1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 8, 12, 12, 12, 12, 12, 25, 33, 33, 29, 33, 33, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 5, 5, 5, 8, 8, 12, 12, 25, 25, 33, 33, 33, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 150 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/881 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/881' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1nccn1Cc1ccccc1) `ZINC000464278509.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464278509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000464278509 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1nccn1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 8, 12, 12, 12, 12, 12, 27, 35, 35, 31, 35, 35, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 5, 5, 5, 8, 8, 12, 12, 27, 27, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 156 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464278509 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509 Building ZINC000464278509 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464278509 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 880) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1nccn1Cc1ccccc1) `ZINC000464278509.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464278509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000464278509 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1nccn1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 8, 12, 12, 12, 12, 12, 25, 33, 33, 29, 33, 33, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 5, 5, 5, 8, 8, 12, 12, 25, 25, 33, 33, 33, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 150 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 881) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/881: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1nccn1Cc1ccccc1) `ZINC000464278509.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464278509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000464278509 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1nccn1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 8, 12, 12, 12, 12, 12, 27, 35, 35, 31, 35, 35, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 5, 5, 5, 8, 8, 12, 12, 27, 27, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 156 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464278509 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464278509 Building ZINC000464334074 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464334074 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/882 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCOc1ccc2cc(Br)ccc2c1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000464334074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464334074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000464334074 none CC(C)N(CCOc1ccc2cc(Br)ccc2c1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 2, 3, 4, 5, 15, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 4, 4, 5, 5, 34, 34, 34, 34, 34, 34, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/883 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/883' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCOc1ccc2cc(Br)ccc2c1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000464334074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464334074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000464334074 none CC(C)N(CCOc1ccc2cc(Br)ccc2c1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 4, 5, 6, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 5, 5, 6, 6, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464334074 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074 Building ZINC000464334074 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464334074 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 882) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/882: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCOc1ccc2cc(Br)ccc2c1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000464334074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464334074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000464334074 none CC(C)N(CCOc1ccc2cc(Br)ccc2c1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 2, 3, 4, 5, 15, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 4, 4, 5, 5, 34, 34, 34, 34, 34, 34, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 883) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/883: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCOc1ccc2cc(Br)ccc2c1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000464334074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464334074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000464334074 none CC(C)N(CCOc1ccc2cc(Br)ccc2c1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 4, 5, 6, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 5, 5, 6, 6, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464334074 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464334074 Building ZINC000464362060 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464362060 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/884 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)c1cccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2)c1) `ZINC000464362060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464362060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000464362060 none CS(=O)(=O)c1cccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 37, 47, 47, 37, 14, 37, 37, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 8, 12, 12, 8, 12, 12, 37, 47, 47, 47, 15, 37, 37, 4, 3, 3, 3, 3, 12, 12, 8, 12, 12, 37] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/885 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/885' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)c1cccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2)c1) `ZINC000464362060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464362060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000464362060 none CS(=O)(=O)c1cccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 37, 47, 47, 37, 14, 37, 37, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 14, 14, 8, 14, 14, 37, 47, 47, 47, 16, 37, 37, 4, 3, 3, 3, 3, 14, 14, 8, 14, 14, 37] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 202 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464362060 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060 Building ZINC000464362060 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464362060 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 884) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/884: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)c1cccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2)c1) `ZINC000464362060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464362060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000464362060 none CS(=O)(=O)c1cccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 37, 47, 47, 37, 14, 37, 37, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 8, 12, 12, 8, 12, 12, 37, 47, 47, 47, 15, 37, 37, 4, 3, 3, 3, 3, 12, 12, 8, 12, 12, 37] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 885) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/885: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)c1cccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2)c1) `ZINC000464362060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464362060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000464362060 none CS(=O)(=O)c1cccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 37, 47, 47, 37, 14, 37, 37, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 14, 14, 8, 14, 14, 37, 47, 47, 47, 16, 37, 37, 4, 3, 3, 3, 3, 14, 14, 8, 14, 14, 37] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 202 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464362060 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362060 Building ZINC000464362061 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464362061 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/886 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)c1cccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2)c1) `ZINC000464362061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464362061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000464362061 none CS(=O)(=O)c1cccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 37, 47, 47, 37, 14, 37, 37, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 8, 14, 14, 8, 14, 14, 37, 47, 47, 47, 16, 37, 37, 4, 3, 3, 3, 3, 14, 14, 8, 14, 14, 37] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 205 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/887 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)c1cccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2)c1) `ZINC000464362061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464362061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000464362061 none CS(=O)(=O)c1cccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 37, 47, 47, 37, 14, 37, 37, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 12, 12, 8, 12, 12, 37, 47, 47, 47, 15, 37, 37, 4, 3, 3, 3, 3, 12, 12, 8, 12, 12, 37] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464362061 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061 Building ZINC000464362061 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464362061 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 886) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/886: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)c1cccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2)c1) `ZINC000464362061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464362061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000464362061 none CS(=O)(=O)c1cccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 37, 47, 47, 37, 14, 37, 37, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 8, 14, 14, 8, 14, 14, 37, 47, 47, 47, 16, 37, 37, 4, 3, 3, 3, 3, 14, 14, 8, 14, 14, 37] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 205 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 887) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/887: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)c1cccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2)c1) `ZINC000464362061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464362061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000464362061 none CS(=O)(=O)c1cccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 37, 47, 47, 37, 14, 37, 37, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 12, 12, 8, 12, 12, 37, 47, 47, 47, 15, 37, 37, 4, 3, 3, 3, 3, 12, 12, 8, 12, 12, 37] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464362061 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464362061 Building ZINC000464432936 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464432936 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/888 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](n2cccn2)Cc2ccccc21) `ZINC000464432936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464432936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000464432936 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](n2cccn2)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 4, 4, 1, 1, 1, 3, 9, 11, 14, 14, 14, 14, 40, 40, 40, 40, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 10, 10, 10, 10, 10, 4, 4, 4, 14, 14, 40, 40, 40, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 77 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/889 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](n2cccn2)Cc2ccccc21) `ZINC000464432936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464432936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000464432936 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](n2cccn2)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 7, 12, 12, 4, 4, 1, 1, 1, 3, 9, 10, 12, 12, 12, 12, 40, 40, 40, 40, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 12, 12, 8, 12, 12, 4, 4, 4, 12, 12, 40, 40, 40, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 94 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464432936 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936 Building ZINC000464432936 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464432936 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 888) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/888: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](n2cccn2)Cc2ccccc21) `ZINC000464432936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464432936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000464432936 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](n2cccn2)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 4, 4, 1, 1, 1, 3, 9, 11, 14, 14, 14, 14, 40, 40, 40, 40, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 10, 10, 10, 10, 10, 4, 4, 4, 14, 14, 40, 40, 40, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 77 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 889) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/889: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](n2cccn2)Cc2ccccc21) `ZINC000464432936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464432936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000464432936 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](n2cccn2)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 7, 12, 12, 4, 4, 1, 1, 1, 3, 9, 10, 12, 12, 12, 12, 40, 40, 40, 40, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 12, 12, 8, 12, 12, 4, 4, 4, 12, 12, 40, 40, 40, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 94 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464432936 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432936 Building ZINC000464432937 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464432937 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/890 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](n2cccn2)Cc2ccccc21) `ZINC000464432937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464432937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000464432937 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](n2cccn2)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 3, 11, 11, 14, 14, 14, 14, 38, 38, 38, 38, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 14, 14, 38, 38, 38, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 92 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/891 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/891' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](n2cccn2)Cc2ccccc21) `ZINC000464432937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464432937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000464432937 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](n2cccn2)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 8, 11, 11, 4, 4, 1, 1, 1, 3, 9, 9, 12, 12, 12, 12, 38, 38, 38, 38, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 11, 11, 11, 11, 11, 4, 4, 4, 12, 12, 38, 38, 38, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 91 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464432937 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937 Building ZINC000464432937 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464432937 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 890) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/890: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](n2cccn2)Cc2ccccc21) `ZINC000464432937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464432937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000464432937 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](n2cccn2)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 3, 11, 11, 14, 14, 14, 14, 38, 38, 38, 38, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 14, 14, 38, 38, 38, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 92 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 891) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/891: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](n2cccn2)Cc2ccccc21) `ZINC000464432937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464432937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000464432937 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](n2cccn2)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 8, 11, 11, 4, 4, 1, 1, 1, 3, 9, 9, 12, 12, 12, 12, 38, 38, 38, 38, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 11, 11, 11, 11, 11, 4, 4, 4, 12, 12, 38, 38, 38, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 91 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464432937 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464432937 Building ZINC000464497531 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464497531 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/892 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)(C)N(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000464497531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464497531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000464497531 none COC(=O)C(C)(C)N(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 6, 20, 2, 6, 6, 2, 2, 4, 6, 6, 4, 6, 6, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 20, 20, 20, 6, 6, 6, 6, 6, 6, 4, 4, 6, 6, 6, 6, 6, 4, 4, 4, 10, 10, 6, 10, 10, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 107 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/893 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/893' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)(C)N(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000464497531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464497531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000464497531 none COC(=O)C(C)(C)N(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 6, 21, 2, 6, 6, 2, 2, 4, 6, 6, 6, 6, 6, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 21, 21, 21, 6, 6, 6, 6, 6, 6, 4, 4, 6, 6, 6, 6, 6, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 98 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464497531 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531 Building ZINC000464497531 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464497531 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 892) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)(C)N(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000464497531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464497531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000464497531 none COC(=O)C(C)(C)N(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 6, 20, 2, 6, 6, 2, 2, 4, 6, 6, 4, 6, 6, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 20, 20, 20, 6, 6, 6, 6, 6, 6, 4, 4, 6, 6, 6, 6, 6, 4, 4, 4, 10, 10, 6, 10, 10, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 107 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 893) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)(C)N(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000464497531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464497531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000464497531 none COC(=O)C(C)(C)N(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 6, 21, 2, 6, 6, 2, 2, 4, 6, 6, 6, 6, 6, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 21, 21, 21, 6, 6, 6, 6, 6, 6, 4, 4, 6, 6, 6, 6, 6, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 98 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464497531 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464497531 Building ZINC000464546849 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464546849 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/894 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2Cl)c(OC)c1) `ZINC000464546849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464546849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000464546849 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2Cl)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 16, 6, 16, 16, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 5, 11, 11, 11, 16, 16, 24, 16, 26, 26, 26, 16, 16, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 5, 11, 24, 24, 24, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 130 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/895 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2Cl)c(OC)c1) `ZINC000464546849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464546849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000464546849 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2Cl)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 16, 7, 16, 16, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 12, 16, 16, 23, 16, 23, 23, 23, 16, 16, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 4, 12, 23, 23, 23, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 124 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464546849 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849 Building ZINC000464546849 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464546849 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 894) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/894: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2Cl)c(OC)c1) `ZINC000464546849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464546849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000464546849 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2Cl)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 16, 6, 16, 16, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 5, 11, 11, 11, 16, 16, 24, 16, 26, 26, 26, 16, 16, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 5, 11, 24, 24, 24, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 130 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 895) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/895: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2Cl)c(OC)c1) `ZINC000464546849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464546849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000464546849 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2Cl)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 16, 7, 16, 16, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 12, 16, 16, 23, 16, 23, 23, 23, 16, 16, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 4, 12, 23, 23, 23, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 124 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464546849 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546849 Building ZINC000464546853 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464546853 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/896 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2Cl)c(OC)c1) `ZINC000464546853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464546853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000464546853 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2Cl)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 16, 7, 16, 16, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 4, 11, 11, 11, 16, 16, 23, 16, 24, 24, 24, 16, 16, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 4, 11, 23, 23, 23, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 121 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/897 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/897' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2Cl)c(OC)c1) `ZINC000464546853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464546853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000464546853 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2Cl)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 18, 5, 18, 18, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 4, 11, 11, 11, 18, 18, 24, 18, 27, 27, 27, 18, 18, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 6, 11, 24, 24, 24, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464546853 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853 Building ZINC000464546853 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464546853 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 896) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/896: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2Cl)c(OC)c1) `ZINC000464546853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464546853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000464546853 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2Cl)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 16, 7, 16, 16, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 4, 11, 11, 11, 16, 16, 23, 16, 24, 24, 24, 16, 16, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 4, 11, 23, 23, 23, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 121 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 897) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2Cl)c(OC)c1) `ZINC000464546853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464546853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000464546853 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccccc2Cl)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 18, 5, 18, 18, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 4, 11, 11, 11, 18, 18, 24, 18, 27, 27, 27, 18, 18, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 6, 11, 24, 24, 24, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464546853 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464546853 Building ZINC000464583131 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464583131 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/898 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc2ccc(Br)cc2[nH]1) `ZINC000464583131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464583131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000464583131 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc2ccc(Br)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 17, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 13, 13, 5, 13, 13, 5, 5, 1, 1, 1, 1, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 13, 13, 5, 13, 13, 5, 5, 5, 10, 11, 11, 11] 23 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 59 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/899 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/899' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc2ccc(Br)cc2[nH]1) `ZINC000464583131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464583131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000464583131 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc2ccc(Br)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 17, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 13, 13, 5, 13, 13, 5, 5, 1, 1, 1, 1, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 13, 13, 9, 13, 13, 5, 5, 5, 10, 11, 11, 11] 23 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464583131 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131 Building ZINC000464583131 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464583131 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 898) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/898: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc2ccc(Br)cc2[nH]1) `ZINC000464583131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464583131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000464583131 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc2ccc(Br)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 17, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 13, 13, 5, 13, 13, 5, 5, 1, 1, 1, 1, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 13, 13, 5, 13, 13, 5, 5, 5, 10, 11, 11, 11] 23 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 59 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 899) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/899: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc2ccc(Br)cc2[nH]1) `ZINC000464583131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464583131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000464583131 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc2ccc(Br)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 17, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 13, 13, 5, 13, 13, 5, 5, 1, 1, 1, 1, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 13, 13, 9, 13, 13, 5, 5, 5, 10, 11, 11, 11] 23 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464583131 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464583131 Building ZINC000541929741 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541929741 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/900 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(Cc2ccccc2)c(C)c1[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000541929741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541929741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000541929741 none Cc1nn(Cc2ccccc2)c(C)c1[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 48, 50, 50, 48, 50, 50, 12, 12, 7, 7, 7, 7, 7, 7, 7, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 48, 48, 50, 50, 48, 50, 50, 12, 12, 12, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 57, 55, 56, 52, 53, 54, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/901 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/901' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(Cc2ccccc2)c(C)c1[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000541929741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541929741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000541929741 none Cc1nn(Cc2ccccc2)c(C)c1[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 44, 50, 50, 44, 50, 50, 13, 13, 9, 9, 9, 9, 9, 9, 9, 8, 2, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 44, 44, 50, 50, 44, 50, 50, 13, 13, 13, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 176 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541929741 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741 Building ZINC000541929741 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541929741 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 900) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/900: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(Cc2ccccc2)c(C)c1[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000541929741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541929741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000541929741 none Cc1nn(Cc2ccccc2)c(C)c1[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 48, 50, 50, 48, 50, 50, 12, 12, 7, 7, 7, 7, 7, 7, 7, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 48, 48, 50, 50, 48, 50, 50, 12, 12, 12, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 57, 55, 56, 52, 53, 54, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 901) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(Cc2ccccc2)c(C)c1[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000541929741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541929741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000541929741 none Cc1nn(Cc2ccccc2)c(C)c1[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 44, 50, 50, 44, 50, 50, 13, 13, 9, 9, 9, 9, 9, 9, 9, 8, 2, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 44, 44, 50, 50, 44, 50, 50, 13, 13, 13, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 176 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541929741 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929741 Building ZINC000541929742 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541929742 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/902 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(Cc2ccccc2)c(C)c1[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000541929742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541929742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000541929742 none Cc1nn(Cc2ccccc2)c(C)c1[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 46, 50, 50, 46, 50, 50, 15, 15, 9, 9, 9, 9, 9, 9, 9, 8, 1, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 46, 46, 50, 50, 46, 50, 50, 15, 15, 15, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 174 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/903 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/903' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(Cc2ccccc2)c(C)c1[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000541929742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541929742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000541929742 none Cc1nn(Cc2ccccc2)c(C)c1[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 48, 50, 50, 48, 50, 50, 12, 12, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 48, 48, 50, 50, 48, 50, 50, 12, 12, 12, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 173 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541929742 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742 Building ZINC000541929742 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541929742 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 902) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(Cc2ccccc2)c(C)c1[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000541929742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541929742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000541929742 none Cc1nn(Cc2ccccc2)c(C)c1[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 46, 50, 50, 46, 50, 50, 15, 15, 9, 9, 9, 9, 9, 9, 9, 8, 1, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 46, 46, 50, 50, 46, 50, 50, 15, 15, 15, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 174 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 903) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/903: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(Cc2ccccc2)c(C)c1[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000541929742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541929742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000541929742 none Cc1nn(Cc2ccccc2)c(C)c1[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 48, 50, 50, 48, 50, 50, 12, 12, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 48, 48, 50, 50, 48, 50, 50, 12, 12, 12, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 173 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541929742 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541929742 Building ZINC000541946016 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541946016 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/904 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2cccc(S(C)(=O)=O)c2)cc1) `ZINC000541946016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541946016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000541946016 none Cc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2cccc(S(C)(=O)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 14, 14, 6, 4, 6, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 36, 36, 12, 36, 36, 46, 46, 46, 36, 14, 14, 14, 14, 14, 14, 14, 4, 2, 2, 2, 2, 2, 2, 36, 36, 15, 46, 46, 46, 36, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 222 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/905 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/905' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2cccc(S(C)(=O)=O)c2)cc1) `ZINC000541946016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541946016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000541946016 none Cc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2cccc(S(C)(=O)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 16, 16, 8, 4, 8, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 38, 38, 12, 38, 38, 48, 48, 48, 38, 16, 16, 16, 16, 16, 16, 16, 4, 2, 2, 2, 2, 2, 2, 38, 38, 16, 48, 48, 48, 38, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 248 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541946016 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016 Building ZINC000541946016 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541946016 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 904) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/904: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2cccc(S(C)(=O)=O)c2)cc1) `ZINC000541946016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541946016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000541946016 none Cc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2cccc(S(C)(=O)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 14, 14, 6, 4, 6, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 36, 36, 12, 36, 36, 46, 46, 46, 36, 14, 14, 14, 14, 14, 14, 14, 4, 2, 2, 2, 2, 2, 2, 36, 36, 15, 46, 46, 46, 36, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 222 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 905) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/905: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2cccc(S(C)(=O)=O)c2)cc1) `ZINC000541946016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541946016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000541946016 none Cc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2cccc(S(C)(=O)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 16, 16, 8, 4, 8, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 38, 38, 12, 38, 38, 48, 48, 48, 38, 16, 16, 16, 16, 16, 16, 16, 4, 2, 2, 2, 2, 2, 2, 38, 38, 16, 48, 48, 48, 38, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 248 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541946016 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946016 Building ZINC000541946017 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541946017 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/906 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2cccc(S(C)(=O)=O)c2)cc1) `ZINC000541946017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541946017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000541946017 none Cc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2cccc(S(C)(=O)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 8, 4, 8, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 37, 37, 12, 37, 37, 48, 48, 48, 37, 16, 16, 16, 16, 16, 16, 16, 4, 2, 2, 2, 2, 2, 2, 37, 37, 16, 48, 48, 48, 37, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 197 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/907 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2cccc(S(C)(=O)=O)c2)cc1) `ZINC000541946017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541946017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000541946017 none Cc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2cccc(S(C)(=O)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 6, 4, 6, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 36, 36, 12, 36, 36, 46, 46, 46, 36, 14, 14, 14, 14, 14, 14, 14, 4, 2, 2, 2, 2, 2, 2, 36, 36, 15, 46, 46, 46, 36, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541946017 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017 Building ZINC000541946017 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541946017 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 906) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2cccc(S(C)(=O)=O)c2)cc1) `ZINC000541946017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541946017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000541946017 none Cc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2cccc(S(C)(=O)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 8, 4, 8, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 37, 37, 12, 37, 37, 48, 48, 48, 37, 16, 16, 16, 16, 16, 16, 16, 4, 2, 2, 2, 2, 2, 2, 37, 37, 16, 48, 48, 48, 37, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 197 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 907) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2cccc(S(C)(=O)=O)c2)cc1) `ZINC000541946017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541946017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000541946017 none Cc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2cccc(S(C)(=O)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 6, 4, 6, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 36, 36, 12, 36, 36, 46, 46, 46, 36, 14, 14, 14, 14, 14, 14, 14, 4, 2, 2, 2, 2, 2, 2, 36, 36, 15, 46, 46, 46, 36, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541946017 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541946017 Building ZINC000541937835 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541937835 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/908 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2F)c(C)c1[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000541937835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541937835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000541937835 none Cc1nn(c2ccccc2F)c(C)c1[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 5, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 14, 14, 10, 10, 10, 10, 10, 10, 10, 9, 1, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 50, 50, 50, 50, 14, 14, 14, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 79 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/909 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/909' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2F)c(C)c1[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000541937835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541937835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000541937835 none Cc1nn(c2ccccc2F)c(C)c1[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 5, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 50, 50, 43, 50, 50, 50, 16, 16, 10, 10, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 114 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541937835 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835 Building ZINC000541937835 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541937835 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 908) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/908: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2F)c(C)c1[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000541937835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541937835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000541937835 none Cc1nn(c2ccccc2F)c(C)c1[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 5, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 14, 14, 10, 10, 10, 10, 10, 10, 10, 9, 1, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 50, 50, 50, 50, 14, 14, 14, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 79 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 909) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/909: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2F)c(C)c1[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000541937835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541937835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000541937835 none Cc1nn(c2ccccc2F)c(C)c1[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 5, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 50, 50, 43, 50, 50, 50, 16, 16, 10, 10, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 114 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541937835 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937835 Building ZINC000541937848 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541937848 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/910 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2F)c(C)c1[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000541937848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541937848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000541937848 none Cc1nn(c2ccccc2F)c(C)c1[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 5, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 50, 50, 15, 50, 50, 50, 15, 15, 9, 9, 9, 9, 9, 9, 9, 8, 2, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 50, 50, 50, 50, 15, 15, 15, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 194 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/911 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/911' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2F)c(C)c1[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000541937848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541937848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000541937848 none Cc1nn(c2ccccc2F)c(C)c1[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 5, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 50, 50, 15, 50, 50, 50, 15, 15, 11, 11, 11, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 50, 50, 50, 50, 15, 15, 15, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541937848 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848 Building ZINC000541937848 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541937848 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 910) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/910: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2F)c(C)c1[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000541937848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541937848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000541937848 none Cc1nn(c2ccccc2F)c(C)c1[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 5, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 50, 50, 15, 50, 50, 50, 15, 15, 9, 9, 9, 9, 9, 9, 9, 8, 2, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 50, 50, 50, 50, 15, 15, 15, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 194 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 911) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/911: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2F)c(C)c1[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000541937848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541937848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000541937848 none Cc1nn(c2ccccc2F)c(C)c1[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 5, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 50, 50, 15, 50, 50, 50, 15, 15, 11, 11, 11, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 50, 50, 50, 50, 15, 15, 15, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541937848 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541937848 Building ZINC000541961233 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000541961233 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/912 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(Br)cc2)CC1) `ZINC000541961233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541961233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541961233 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 4, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/913 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/913' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(Br)cc2)CC1) `ZINC000541961233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541961233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541961233 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 4, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/914 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/914' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(Br)cc2)CC1) `ZINC000541961233.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000541961233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541961233 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 6, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 23, 23, 2, 2, 2, 2, 2, 2, 3, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/915 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/915' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(Br)cc2)CC1) `ZINC000541961233.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000541961233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541961233 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 4, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541961233 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 Building ZINC000541961233 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000541961233 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 912) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(Br)cc2)CC1) `ZINC000541961233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541961233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541961233 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 4, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 913) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(Br)cc2)CC1) `ZINC000541961233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541961233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541961233 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 4, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 914) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(Br)cc2)CC1) `ZINC000541961233.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000541961233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541961233 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 6, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 23, 23, 2, 2, 2, 2, 2, 2, 3, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 915) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(Br)cc2)CC1) `ZINC000541961233.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000541961233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541961233 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 4, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541961233 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 Building ZINC000541961233 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000541961233 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 912) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(Br)cc2)CC1) `ZINC000541961233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541961233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541961233 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 4, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 913) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(Br)cc2)CC1) `ZINC000541961233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541961233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541961233 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 4, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 914) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(Br)cc2)CC1) `ZINC000541961233.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000541961233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541961233 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 6, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 23, 23, 2, 2, 2, 2, 2, 2, 3, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 915) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(Br)cc2)CC1) `ZINC000541961233.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000541961233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541961233 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 4, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541961233 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 Building ZINC000541961233 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000541961233 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 912) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(Br)cc2)CC1) `ZINC000541961233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541961233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541961233 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 4, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 913) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(Br)cc2)CC1) `ZINC000541961233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541961233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541961233 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](Cc2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 4, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 914) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(Br)cc2)CC1) `ZINC000541961233.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000541961233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541961233 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 6, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 23, 23, 2, 2, 2, 2, 2, 2, 3, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 915) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(Br)cc2)CC1) `ZINC000541961233.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000541961233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541961233 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](Cc2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 4, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541961233 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541961233 Building ZINC000541953715 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541953715 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/916 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc(NC(=O)Cn2cc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cn2)cc1) `ZINC000541953715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541953715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541953715 none CSc1ccc(NC(=O)Cn2cc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 47, 20, 20, 18, 20, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 7, 47, 47, 50, 50, 50, 47, 47, 20, 18, 18, 7, 3, 2, 2, 2, 2, 2, 2, 7, 47, 47] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/917 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/917' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc(NC(=O)Cn2cc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cn2)cc1) `ZINC000541953715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541953715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541953715 none CSc1ccc(NC(=O)Cn2cc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 48, 16, 16, 16, 16, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 7, 48, 48, 50, 50, 50, 48, 48, 16, 16, 16, 7, 3, 2, 2, 2, 2, 2, 2, 7, 48, 48] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541953715 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715 Building ZINC000541953715 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541953715 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 916) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/916: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc(NC(=O)Cn2cc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cn2)cc1) `ZINC000541953715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541953715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541953715 none CSc1ccc(NC(=O)Cn2cc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 47, 20, 20, 18, 20, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 7, 47, 47, 50, 50, 50, 47, 47, 20, 18, 18, 7, 3, 2, 2, 2, 2, 2, 2, 7, 47, 47] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 917) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/917: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc(NC(=O)Cn2cc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cn2)cc1) `ZINC000541953715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541953715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541953715 none CSc1ccc(NC(=O)Cn2cc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 48, 16, 16, 16, 16, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 7, 48, 48, 50, 50, 50, 48, 48, 16, 16, 16, 7, 3, 2, 2, 2, 2, 2, 2, 7, 48, 48] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541953715 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541953715 Building ZINC000541958860 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541958860 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/918 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)Nc2ccc(F)cc2)cc1) `ZINC000541958860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541958860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541958860 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)Nc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 17, 31, 31, 24, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 2, 2, 2, 2, 2, 2, 3, 17, 17, 31, 31, 50, 50, 50, 50, 50, 31, 31] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/919 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)Nc2ccc(F)cc2)cc1) `ZINC000541958860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541958860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541958860 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)Nc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 17, 31, 31, 22, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 2, 2, 2, 2, 2, 2, 3, 17, 17, 31, 31, 50, 50, 50, 50, 50, 31, 31] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541958860 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860 Building ZINC000541958860 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000541958860 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 918) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/918: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)Nc2ccc(F)cc2)cc1) `ZINC000541958860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000541958860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541958860 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)Nc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 17, 31, 31, 24, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 2, 2, 2, 2, 2, 2, 3, 17, 17, 31, 31, 50, 50, 50, 50, 50, 31, 31] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 919) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)Nc2ccc(F)cc2)cc1) `ZINC000541958860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000541958860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000541958860 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)Nc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 17, 31, 31, 22, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 2, 2, 2, 2, 2, 2, 3, 17, 17, 31, 31, 50, 50, 50, 50, 50, 31, 31] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000541958860 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000541958860 Building ZINC000302954235 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000302954235 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/920 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1c(Cl)cccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000302954235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000302954235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000302954235 none COCCOc1c(Cl)cccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 25, 17, 8, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 38, 38, 38, 25, 25, 17, 17, 5, 5, 5, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/921 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1c(Cl)cccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000302954235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000302954235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000302954235 none COCCOc1c(Cl)cccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 25, 17, 8, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 38, 38, 38, 25, 25, 17, 17, 5, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000302954235 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235 Building ZINC000302954235 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000302954235 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 920) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1c(Cl)cccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000302954235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000302954235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000302954235 none COCCOc1c(Cl)cccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 25, 17, 8, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 38, 38, 38, 25, 25, 17, 17, 5, 5, 5, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 921) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1c(Cl)cccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000302954235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000302954235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000302954235 none COCCOc1c(Cl)cccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 25, 17, 8, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 38, 38, 38, 25, 25, 17, 17, 5, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000302954235 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302954235 Building ZINC000302989120 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000302989120 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/922 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](Cc2cccs2)CC1) `ZINC000302989120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000302989120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000302989120 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](Cc2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 21, 21, 21, 21, 21, 34, 49, 49, 49, 49, 21, 21, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 21, 21, 21, 21, 34, 34, 49, 49, 49, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/923 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/923' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](Cc2cccs2)CC1) `ZINC000302989120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000302989120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000302989120 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](Cc2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 20, 20, 20, 20, 20, 35, 50, 50, 50, 50, 20, 20, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 8, 8, 20, 20, 20, 20, 35, 35, 50, 50, 50, 20, 20, 20, 20] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/924 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/924' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](Cc2cccs2)CC1) `ZINC000302989120.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000302989120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000302989120 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](Cc2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 21, 21, 21, 21, 21, 35, 49, 49, 49, 49, 21, 21, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 21, 21, 21, 21, 35, 35, 49, 49, 49, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/925 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/925' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](Cc2cccs2)CC1) `ZINC000302989120.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000302989120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000302989120 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](Cc2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 19, 19, 19, 19, 19, 33, 47, 47, 47, 47, 19, 19, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 10, 10, 19, 19, 19, 19, 33, 33, 47, 47, 47, 19, 19, 19, 19] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000302989120 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 Building ZINC000302989120 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000302989120 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 922) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](Cc2cccs2)CC1) `ZINC000302989120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000302989120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000302989120 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](Cc2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 21, 21, 21, 21, 21, 34, 49, 49, 49, 49, 21, 21, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 21, 21, 21, 21, 34, 34, 49, 49, 49, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 923) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](Cc2cccs2)CC1) `ZINC000302989120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000302989120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000302989120 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](Cc2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 20, 20, 20, 20, 20, 35, 50, 50, 50, 50, 20, 20, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 8, 8, 20, 20, 20, 20, 35, 35, 50, 50, 50, 20, 20, 20, 20] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 924) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](Cc2cccs2)CC1) `ZINC000302989120.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000302989120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000302989120 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](Cc2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 21, 21, 21, 21, 21, 35, 49, 49, 49, 49, 21, 21, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 21, 21, 21, 21, 35, 35, 49, 49, 49, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 925) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](Cc2cccs2)CC1) `ZINC000302989120.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000302989120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000302989120 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](Cc2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 19, 19, 19, 19, 19, 33, 47, 47, 47, 47, 19, 19, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 10, 10, 19, 19, 19, 19, 33, 33, 47, 47, 47, 19, 19, 19, 19] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000302989120 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 Building ZINC000302989120 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000302989120 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 922) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](Cc2cccs2)CC1) `ZINC000302989120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000302989120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000302989120 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](Cc2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 21, 21, 21, 21, 21, 34, 49, 49, 49, 49, 21, 21, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 21, 21, 21, 21, 34, 34, 49, 49, 49, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 923) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](Cc2cccs2)CC1) `ZINC000302989120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000302989120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000302989120 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](Cc2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 20, 20, 20, 20, 20, 35, 50, 50, 50, 50, 20, 20, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 8, 8, 20, 20, 20, 20, 35, 35, 50, 50, 50, 20, 20, 20, 20] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 924) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](Cc2cccs2)CC1) `ZINC000302989120.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000302989120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000302989120 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](Cc2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 21, 21, 21, 21, 21, 35, 49, 49, 49, 49, 21, 21, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 21, 21, 21, 21, 35, 35, 49, 49, 49, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 925) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](Cc2cccs2)CC1) `ZINC000302989120.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000302989120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000302989120 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](Cc2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 19, 19, 19, 19, 19, 33, 47, 47, 47, 47, 19, 19, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 10, 10, 19, 19, 19, 19, 33, 33, 47, 47, 47, 19, 19, 19, 19] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000302989120 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 Building ZINC000302989120 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000302989120 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 922) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](Cc2cccs2)CC1) `ZINC000302989120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000302989120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000302989120 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](Cc2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 21, 21, 21, 21, 21, 34, 49, 49, 49, 49, 21, 21, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 21, 21, 21, 21, 34, 34, 49, 49, 49, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 923) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](Cc2cccs2)CC1) `ZINC000302989120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000302989120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000302989120 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](Cc2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 20, 20, 20, 20, 20, 35, 50, 50, 50, 50, 20, 20, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 8, 8, 20, 20, 20, 20, 35, 35, 50, 50, 50, 20, 20, 20, 20] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 924) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](Cc2cccs2)CC1) `ZINC000302989120.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000302989120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000302989120 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](Cc2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 21, 21, 21, 21, 21, 35, 49, 49, 49, 49, 21, 21, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 21, 21, 21, 21, 35, 35, 49, 49, 49, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 925) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](Cc2cccs2)CC1) `ZINC000302989120.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000302989120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000302989120 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](Cc2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 19, 19, 19, 19, 19, 33, 47, 47, 47, 47, 19, 19, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 10, 10, 19, 19, 19, 19, 33, 33, 47, 47, 47, 19, 19, 19, 19] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000302989120 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000302989120 Building ZINC000542007550 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542007550 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/926 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CCO)cc1) `ZINC000542007550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542007550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000542007550 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CCO)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 10, 11, 5, 5, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 5, 5, 10, 10, 11, 11, 33, 5, 5] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/927 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/927' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(CCO)cc1) `ZINC000542007550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542007550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000542007550 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(CCO)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 4, 11, 12, 6, 6, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 2, 6, 6, 11, 11, 12, 12, 36, 6, 6] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 132 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000542007550 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550 Building ZINC000542007550 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542007550 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 926) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CCO)cc1) `ZINC000542007550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542007550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000542007550 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CCO)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 10, 11, 5, 5, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 5, 5, 10, 10, 11, 11, 33, 5, 5] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 927) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/927: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(CCO)cc1) `ZINC000542007550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542007550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000542007550 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(CCO)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 4, 11, 12, 6, 6, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 2, 6, 6, 11, 11, 12, 12, 36, 6, 6] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 132 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000542007550 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542007550 Building ZINC000464906074 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000464906074 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/928 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1) `ZINC000464906074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464906074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906074 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 17, 17, 17, 20, 29, 29, 20, 29, 29, 17, 17, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 20, 20, 29, 29, 22, 29, 29, 17, 17, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/929 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1) `ZINC000464906074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464906074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906074 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 7, 8, 12, 12, 12, 12, 12, 12, 12, 20, 30, 30, 20, 30, 30, 12, 12, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 20, 20, 30, 30, 24, 30, 30, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 151 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/930 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/930' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1) `ZINC000464906074.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000464906074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906074 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 17, 17, 17, 20, 29, 29, 20, 29, 29, 17, 17, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 20, 20, 29, 29, 22, 29, 29, 17, 17, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/931 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/931' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1) `ZINC000464906074.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000464906074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906074 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 7, 8, 12, 12, 12, 12, 12, 12, 12, 20, 30, 30, 20, 30, 30, 12, 12, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 20, 20, 30, 30, 24, 30, 30, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 151 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464906074 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 Building ZINC000464906074 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000464906074 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 928) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/928: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1) `ZINC000464906074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464906074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906074 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 17, 17, 17, 20, 29, 29, 20, 29, 29, 17, 17, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 20, 20, 29, 29, 22, 29, 29, 17, 17, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 929) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/929: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1) `ZINC000464906074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464906074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906074 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 7, 8, 12, 12, 12, 12, 12, 12, 12, 20, 30, 30, 20, 30, 30, 12, 12, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 20, 20, 30, 30, 24, 30, 30, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 151 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 930) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1) `ZINC000464906074.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000464906074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906074 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 17, 17, 17, 20, 29, 29, 20, 29, 29, 17, 17, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 20, 20, 29, 29, 22, 29, 29, 17, 17, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 931) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1) `ZINC000464906074.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000464906074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906074 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 7, 8, 12, 12, 12, 12, 12, 12, 12, 20, 30, 30, 20, 30, 30, 12, 12, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 20, 20, 30, 30, 24, 30, 30, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 151 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464906074 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 Building ZINC000464906074 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000464906074 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 928) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/928: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1) `ZINC000464906074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464906074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906074 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 17, 17, 17, 20, 29, 29, 20, 29, 29, 17, 17, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 20, 20, 29, 29, 22, 29, 29, 17, 17, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 929) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/929: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1) `ZINC000464906074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464906074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906074 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 7, 8, 12, 12, 12, 12, 12, 12, 12, 20, 30, 30, 20, 30, 30, 12, 12, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 20, 20, 30, 30, 24, 30, 30, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 151 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 930) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1) `ZINC000464906074.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000464906074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906074 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 17, 17, 17, 20, 29, 29, 20, 29, 29, 17, 17, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 20, 20, 29, 29, 22, 29, 29, 17, 17, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 931) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1) `ZINC000464906074.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000464906074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906074 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 7, 8, 12, 12, 12, 12, 12, 12, 12, 20, 30, 30, 20, 30, 30, 12, 12, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 20, 20, 30, 30, 24, 30, 30, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 151 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464906074 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 Building ZINC000464906074 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000464906074 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 928) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/928: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1) `ZINC000464906074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464906074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906074 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 17, 17, 17, 20, 29, 29, 20, 29, 29, 17, 17, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 20, 20, 29, 29, 22, 29, 29, 17, 17, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 929) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/929: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1) `ZINC000464906074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464906074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906074 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 7, 8, 12, 12, 12, 12, 12, 12, 12, 20, 30, 30, 20, 30, 30, 12, 12, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 20, 20, 30, 30, 24, 30, 30, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 151 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 930) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1) `ZINC000464906074.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000464906074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906074 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 17, 17, 17, 20, 29, 29, 20, 29, 29, 17, 17, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 20, 20, 29, 29, 22, 29, 29, 17, 17, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 931) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1) `ZINC000464906074.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000464906074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906074 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 7, 8, 12, 12, 12, 12, 12, 12, 12, 20, 30, 30, 20, 30, 30, 12, 12, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 20, 20, 30, 30, 24, 30, 30, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 151 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464906074 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906074 Building ZINC000464906075 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000464906075 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/932 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1) `ZINC000464906075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464906075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906075 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 15, 15, 15, 23, 32, 32, 23, 32, 32, 15, 15, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 23, 23, 32, 32, 23, 32, 32, 15, 15, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/933 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1) `ZINC000464906075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464906075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906075 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 8, 12, 14, 14, 14, 14, 14, 14, 14, 20, 29, 29, 20, 29, 29, 14, 14, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 20, 20, 29, 29, 20, 29, 29, 14, 14, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 125 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/934 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/934' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1) `ZINC000464906075.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000464906075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906075 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 15, 15, 15, 23, 32, 32, 23, 32, 32, 15, 15, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 23, 23, 32, 32, 23, 32, 32, 15, 15, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/935 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/935' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1) `ZINC000464906075.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000464906075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906075 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 8, 12, 14, 14, 14, 14, 14, 14, 14, 20, 29, 29, 20, 29, 29, 14, 14, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 20, 20, 29, 29, 20, 29, 29, 14, 14, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 125 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464906075 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 Building ZINC000464906075 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000464906075 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 932) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/932: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1) `ZINC000464906075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464906075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906075 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 15, 15, 15, 23, 32, 32, 23, 32, 32, 15, 15, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 23, 23, 32, 32, 23, 32, 32, 15, 15, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 933) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1) `ZINC000464906075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464906075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906075 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 8, 12, 14, 14, 14, 14, 14, 14, 14, 20, 29, 29, 20, 29, 29, 14, 14, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 20, 20, 29, 29, 20, 29, 29, 14, 14, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 125 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 934) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1) `ZINC000464906075.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000464906075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906075 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 15, 15, 15, 23, 32, 32, 23, 32, 32, 15, 15, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 23, 23, 32, 32, 23, 32, 32, 15, 15, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 935) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1) `ZINC000464906075.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000464906075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906075 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 8, 12, 14, 14, 14, 14, 14, 14, 14, 20, 29, 29, 20, 29, 29, 14, 14, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 20, 20, 29, 29, 20, 29, 29, 14, 14, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 125 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464906075 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 Building ZINC000464906075 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000464906075 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 932) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/932: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1) `ZINC000464906075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464906075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906075 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 15, 15, 15, 23, 32, 32, 23, 32, 32, 15, 15, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 23, 23, 32, 32, 23, 32, 32, 15, 15, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 933) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1) `ZINC000464906075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464906075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906075 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 8, 12, 14, 14, 14, 14, 14, 14, 14, 20, 29, 29, 20, 29, 29, 14, 14, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 20, 20, 29, 29, 20, 29, 29, 14, 14, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 125 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 934) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1) `ZINC000464906075.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000464906075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906075 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 15, 15, 15, 23, 32, 32, 23, 32, 32, 15, 15, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 23, 23, 32, 32, 23, 32, 32, 15, 15, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 935) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1) `ZINC000464906075.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000464906075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906075 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 8, 12, 14, 14, 14, 14, 14, 14, 14, 20, 29, 29, 20, 29, 29, 14, 14, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 20, 20, 29, 29, 20, 29, 29, 14, 14, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 125 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464906075 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 Building ZINC000464906075 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000464906075 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 932) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/932: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1) `ZINC000464906075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464906075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906075 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 15, 15, 15, 23, 32, 32, 23, 32, 32, 15, 15, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 23, 23, 32, 32, 23, 32, 32, 15, 15, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 933) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1) `ZINC000464906075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464906075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906075 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 8, 12, 14, 14, 14, 14, 14, 14, 14, 20, 29, 29, 20, 29, 29, 14, 14, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 20, 20, 29, 29, 20, 29, 29, 14, 14, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 125 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 934) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1) `ZINC000464906075.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000464906075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906075 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 15, 15, 15, 23, 32, 32, 23, 32, 32, 15, 15, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 23, 23, 32, 32, 23, 32, 32, 15, 15, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 935) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1) `ZINC000464906075.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000464906075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464906075 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)N(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 8, 12, 14, 14, 14, 14, 14, 14, 14, 20, 29, 29, 20, 29, 29, 14, 14, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 20, 20, 29, 29, 20, 29, 29, 14, 14, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 125 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464906075 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464906075 Building ZINC000464909326 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464909326 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/936 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1noc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1) `ZINC000464909326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464909326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000464909326 none COc1ccccc1c1noc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 47, 47, 47, 29, 47, 47, 14, 14, 14, 14, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 14, 48, 48, 48, 47, 47, 47, 47, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 152 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/937 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/937' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1noc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1) `ZINC000464909326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464909326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000464909326 none COc1ccccc1c1noc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 26, 45, 45, 16, 16, 16, 16, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 16, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464909326 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326 Building ZINC000464909326 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464909326 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 936) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/936: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1noc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1) `ZINC000464909326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464909326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000464909326 none COc1ccccc1c1noc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 47, 47, 47, 29, 47, 47, 14, 14, 14, 14, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 14, 48, 48, 48, 47, 47, 47, 47, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 152 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 937) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1noc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1) `ZINC000464909326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464909326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000464909326 none COc1ccccc1c1noc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 26, 45, 45, 16, 16, 16, 16, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 16, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464909326 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909326 Building ZINC000464909327 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464909327 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/938 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1noc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1) `ZINC000464909327.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464909327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000464909327 none COc1ccccc1c1noc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 26, 46, 46, 15, 15, 15, 15, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 15, 46, 46, 46, 46, 46, 46, 46, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/939 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/939' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1noc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1) `ZINC000464909327.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464909327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000464909327 none COc1ccccc1c1noc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 45, 45, 30, 45, 45, 14, 14, 14, 14, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 14, 46, 46, 46, 45, 45, 45, 45, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 148 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464909327 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327 Building ZINC000464909327 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464909327 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 938) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1noc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1) `ZINC000464909327.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464909327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000464909327 none COc1ccccc1c1noc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 26, 46, 46, 15, 15, 15, 15, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 15, 46, 46, 46, 46, 46, 46, 46, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 939) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/939: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1noc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1) `ZINC000464909327.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464909327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000464909327 none COc1ccccc1c1noc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 45, 45, 30, 45, 45, 14, 14, 14, 14, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 14, 46, 46, 46, 45, 45, 45, 45, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 148 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464909327 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464909327 Building ZINC000464912446 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464912446 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/940 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2cccc(F)c2)no1) `ZINC000464912446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464912446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000464912446 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2cccc(F)c2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 15, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 28, 28, 28, 49, 49, 49, 49, 49, 49, 28, 28, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 3, 4, 4, 4, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/941 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/941' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2cccc(F)c2)no1) `ZINC000464912446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464912446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000464912446 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2cccc(F)c2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 15, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 28, 28, 28, 48, 48, 48, 48, 48, 48, 28, 28, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 5, 5, 5, 48, 48, 48, 48] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464912446 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446 Building ZINC000464912446 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464912446 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 940) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/940: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2cccc(F)c2)no1) `ZINC000464912446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464912446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000464912446 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2cccc(F)c2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 15, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 28, 28, 28, 49, 49, 49, 49, 49, 49, 28, 28, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 3, 4, 4, 4, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 941) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2cccc(F)c2)no1) `ZINC000464912446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464912446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000464912446 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2cccc(F)c2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 15, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 28, 28, 28, 48, 48, 48, 48, 48, 48, 28, 28, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 5, 5, 5, 48, 48, 48, 48] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464912446 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912446 Building ZINC000464912451 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464912451 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/942 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2cccc(F)c2)no1) `ZINC000464912451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464912451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000464912451 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2cccc(F)c2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 15, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 28, 28, 28, 46, 46, 46, 46, 46, 46, 28, 28, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 5, 5, 5, 46, 46, 46, 46] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/943 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2cccc(F)c2)no1) `ZINC000464912451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464912451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000464912451 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2cccc(F)c2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 15, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 28, 28, 28, 49, 49, 49, 49, 49, 49, 28, 28, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 4, 4, 4, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 99 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464912451 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451 Building ZINC000464912451 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464912451 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 942) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/942: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2cccc(F)c2)no1) `ZINC000464912451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464912451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000464912451 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2cccc(F)c2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 15, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 28, 28, 28, 46, 46, 46, 46, 46, 46, 28, 28, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 5, 5, 5, 46, 46, 46, 46] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 943) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/943: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2cccc(F)c2)no1) `ZINC000464912451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464912451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000464912451 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2cccc(F)c2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 15, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 28, 28, 28, 49, 49, 49, 49, 49, 49, 28, 28, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 4, 4, 4, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 99 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464912451 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464912451 Building ZINC000464926194 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464926194 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/944 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2noc([C@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)c1) `ZINC000464926194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464926194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000464926194 none COc1cccc(c2noc([C@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 32, 32, 32, 32, 32, 19, 19, 19, 19, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 19, 32, 44, 44, 44, 32, 32, 32, 2, 2, 2, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 32] 50 rigid atoms, others: [11, 43, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 85 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/945 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/945' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2noc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)c1) `ZINC000464926194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464926194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000464926194 none COc1cccc(c2noc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 33, 33, 33, 33, 33, 19, 19, 19, 19, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 19, 33, 40, 40, 40, 33, 33, 33, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 33] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464926194 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194 Building ZINC000464926194 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464926194 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 944) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2noc([C@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)c1) `ZINC000464926194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464926194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000464926194 none COc1cccc(c2noc([C@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 32, 32, 32, 32, 32, 19, 19, 19, 19, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 19, 32, 44, 44, 44, 32, 32, 32, 2, 2, 2, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 32] 50 rigid atoms, others: [11, 43, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 85 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 945) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2noc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)c1) `ZINC000464926194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464926194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000464926194 none COc1cccc(c2noc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 33, 33, 33, 33, 33, 19, 19, 19, 19, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 19, 33, 40, 40, 40, 33, 33, 33, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 33] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464926194 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926194 Building ZINC000464926195 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464926195 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/946 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2noc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)c1) `ZINC000464926195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464926195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000464926195 none COc1cccc(c2noc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 32, 32, 32, 32, 32, 19, 19, 19, 19, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 19, 32, 40, 40, 40, 32, 32, 32, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 32] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/947 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/947' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2noc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)c1) `ZINC000464926195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464926195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000464926195 none COc1cccc(c2noc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 33, 33, 33, 33, 33, 19, 19, 19, 19, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 19, 33, 45, 45, 45, 33, 33, 33, 2, 2, 2, 1, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 33] 50 rigid atoms, others: [11, 43, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464926195 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195 Building ZINC000464926195 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464926195 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 946) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2noc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)c1) `ZINC000464926195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464926195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000464926195 none COc1cccc(c2noc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 32, 32, 32, 32, 32, 19, 19, 19, 19, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 19, 32, 40, 40, 40, 32, 32, 32, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 32] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 947) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/947: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2noc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)c1) `ZINC000464926195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464926195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000464926195 none COc1cccc(c2noc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 33, 33, 33, 33, 33, 19, 19, 19, 19, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 19, 33, 45, 45, 45, 33, 33, 33, 2, 2, 2, 1, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 33] 50 rigid atoms, others: [11, 43, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464926195 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464926195 Building ZINC000303016544 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303016544 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/948 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C2(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CCOCC2)cc1) `ZINC000303016544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303016544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000303016544 none COc1ccc(C2(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CCOCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 26, 14, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 26, 26, 26, 26, 26, 38, 38, 38, 38, 38, 38, 38, 8, 8, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 26, 26, 26, 26, 26, 26, 26, 26, 38, 38] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/949 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/949' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C2(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CCOCC2)cc1) `ZINC000303016544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303016544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000303016544 none COc1ccc(C2(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CCOCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 26, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 26, 26, 26, 26, 26, 37, 37, 37, 37, 37, 37, 37, 7, 7, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 26, 26, 26, 26, 26, 26, 26, 26, 37, 37] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000303016544 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544 Building ZINC000303016544 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303016544 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 948) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/948: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C2(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CCOCC2)cc1) `ZINC000303016544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303016544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000303016544 none COc1ccc(C2(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CCOCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 26, 14, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 26, 26, 26, 26, 26, 38, 38, 38, 38, 38, 38, 38, 8, 8, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 26, 26, 26, 26, 26, 26, 26, 26, 38, 38] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 949) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/949: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C2(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CCOCC2)cc1) `ZINC000303016544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303016544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000303016544 none COc1ccc(C2(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CCOCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 26, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 26, 26, 26, 26, 26, 37, 37, 37, 37, 37, 37, 37, 7, 7, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 26, 26, 26, 26, 26, 26, 26, 26, 37, 37] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000303016544 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303016544 Building ZINC000542058520 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542058520 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/950 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](n2ccc(C(F)(F)F)n2)C1) `ZINC000542058520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542058520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000542058520 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](n2ccc(C(F)(F)F)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 5, 15, 15, 15, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 34, 34, 34, 34, 34, 34, 34, 34, 7, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 2, 7, 7, 7, 7, 7, 7, 34, 34, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 64 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/951 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/951' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](n2ccc(C(F)(F)F)n2)C1) `ZINC000542058520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542058520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000542058520 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](n2ccc(C(F)(F)F)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 5, 15, 15, 15, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 3, 3, 1, 1, 1, 1, 6, 7, 8, 8, 8, 8, 8, 8, 34, 34, 34, 34, 34, 34, 34, 34, 8, 3, 3, 3, 7, 7, 7, 7, 7, 3, 3, 3, 8, 8, 8, 8, 8, 8, 34, 34, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 56 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000542058520 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520 Building ZINC000542058520 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542058520 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 950) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/950: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](n2ccc(C(F)(F)F)n2)C1) `ZINC000542058520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542058520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000542058520 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](n2ccc(C(F)(F)F)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 5, 15, 15, 15, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 34, 34, 34, 34, 34, 34, 34, 34, 7, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 2, 7, 7, 7, 7, 7, 7, 34, 34, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 64 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 951) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/951: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](n2ccc(C(F)(F)F)n2)C1) `ZINC000542058520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542058520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000542058520 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](n2ccc(C(F)(F)F)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 5, 15, 15, 15, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 3, 3, 1, 1, 1, 1, 6, 7, 8, 8, 8, 8, 8, 8, 34, 34, 34, 34, 34, 34, 34, 34, 8, 3, 3, 3, 7, 7, 7, 7, 7, 3, 3, 3, 8, 8, 8, 8, 8, 8, 34, 34, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 56 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000542058520 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058520 Building ZINC000542058523 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542058523 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/952 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](n2ccc(C(F)(F)F)n2)C1) `ZINC000542058523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542058523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000542058523 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](n2ccc(C(F)(F)F)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 5, 15, 15, 15, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 37, 37, 37, 37, 37, 37, 37, 37, 7, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 7, 7, 7, 7, 7, 7, 37, 37, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/953 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/953' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](n2ccc(C(F)(F)F)n2)C1) `ZINC000542058523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542058523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000542058523 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](n2ccc(C(F)(F)F)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 5, 15, 15, 15, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 2, 2, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 37, 37, 37, 37, 37, 37, 37, 37, 7, 2, 2, 2, 5, 5, 5, 5, 5, 2, 2, 2, 7, 7, 7, 7, 7, 7, 37, 37, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 58 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000542058523 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523 Building ZINC000542058523 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542058523 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 952) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/952: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](n2ccc(C(F)(F)F)n2)C1) `ZINC000542058523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542058523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000542058523 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](n2ccc(C(F)(F)F)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 5, 15, 15, 15, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 37, 37, 37, 37, 37, 37, 37, 37, 7, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 7, 7, 7, 7, 7, 7, 37, 37, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 953) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/953: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](n2ccc(C(F)(F)F)n2)C1) `ZINC000542058523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542058523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000542058523 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](n2ccc(C(F)(F)F)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 5, 15, 15, 15, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 2, 2, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 37, 37, 37, 37, 37, 37, 37, 37, 7, 2, 2, 2, 5, 5, 5, 5, 5, 2, 2, 2, 7, 7, 7, 7, 7, 7, 37, 37, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 58 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000542058523 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542058523 Building ZINC000542070551 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542070551 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/954 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)CCC1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000542070551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542070551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000542070551 none CCN(CC)C(=O)CCC1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 26, 26, 26, 36, 11, 26, 11, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 3, 3, 37, 37, 37, 37, 37, 36, 36, 36, 36, 36, 11, 11, 11, 11, 3, 3, 3, 3, 3, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/955 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)CCC1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000542070551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542070551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000542070551 none CCN(CC)C(=O)CCC1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 27, 27, 27, 35, 14, 27, 13, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 4, 37, 37, 37, 37, 37, 35, 35, 35, 35, 35, 14, 14, 13, 13, 4, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000542070551 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551 Building ZINC000542070551 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542070551 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 954) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/954: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)CCC1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000542070551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542070551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000542070551 none CCN(CC)C(=O)CCC1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 26, 26, 26, 36, 11, 26, 11, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 3, 3, 37, 37, 37, 37, 37, 36, 36, 36, 36, 36, 11, 11, 11, 11, 3, 3, 3, 3, 3, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 955) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/955: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)CCC1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000542070551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542070551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000542070551 none CCN(CC)C(=O)CCC1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 27, 27, 27, 35, 14, 27, 13, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 4, 37, 37, 37, 37, 37, 35, 35, 35, 35, 35, 14, 14, 13, 13, 4, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000542070551 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542070551 Building ZINC000464974634 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000464974634 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/956 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C[C@H]1CC[N@](c2ccccn2)CC1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000464974634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464974634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000464974634 none CCN(C[C@H]1CC[N@](c2ccccn2)CC1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 7, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 11, 11, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 3, 3, 3, 3, 3, 5, 5, 11, 11, 11, 11, 17, 17, 17, 17, 11, 11, 11, 11, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 68 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/957 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/957' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C[C@H]1CC[N@@](c2ccccn2)CC1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000464974634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464974634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000464974634 none CCN(C[C@H]1CC[N@@](c2ccccn2)CC1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 6, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 10, 10, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 5, 9, 9, 3, 3, 2, 2, 2, 2, 2, 4, 4, 10, 10, 10, 10, 16, 16, 16, 16, 10, 10, 10, 10, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3] 50 rigid atoms, others: [2, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 64 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/958 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/958' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C[C@H]1CC[N@](c2ccccn2)CC1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000464974634.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000464974634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000464974634 none CCN(C[C@H]1CC[N@](c2ccccn2)CC1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 7, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 9, 9, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 5, 9, 9, 4, 4, 3, 3, 3, 3, 3, 5, 5, 9, 9, 9, 9, 16, 16, 16, 16, 9, 9, 9, 9, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 61 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/959 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/959' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C[C@H]1CC[N@@](c2ccccn2)CC1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000464974634.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000464974634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000464974634 none CCN(C[C@H]1CC[N@@](c2ccccn2)CC1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 7, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 8, 8, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 3, 3, 3, 3, 3, 5, 5, 8, 8, 8, 8, 15, 15, 15, 15, 8, 8, 8, 8, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 61 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464974634 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 Building ZINC000464974634 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000464974634 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 956) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/956: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C[C@H]1CC[N@](c2ccccn2)CC1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000464974634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464974634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000464974634 none CCN(C[C@H]1CC[N@](c2ccccn2)CC1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 7, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 11, 11, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 3, 3, 3, 3, 3, 5, 5, 11, 11, 11, 11, 17, 17, 17, 17, 11, 11, 11, 11, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 68 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 957) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C[C@H]1CC[N@@](c2ccccn2)CC1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000464974634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464974634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000464974634 none CCN(C[C@H]1CC[N@@](c2ccccn2)CC1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 6, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 10, 10, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 5, 9, 9, 3, 3, 2, 2, 2, 2, 2, 4, 4, 10, 10, 10, 10, 16, 16, 16, 16, 10, 10, 10, 10, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3] 50 rigid atoms, others: [2, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 64 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 958) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C[C@H]1CC[N@](c2ccccn2)CC1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000464974634.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000464974634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000464974634 none CCN(C[C@H]1CC[N@](c2ccccn2)CC1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 7, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 9, 9, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 5, 9, 9, 4, 4, 3, 3, 3, 3, 3, 5, 5, 9, 9, 9, 9, 16, 16, 16, 16, 9, 9, 9, 9, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 61 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 959) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C[C@H]1CC[N@@](c2ccccn2)CC1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000464974634.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000464974634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000464974634 none CCN(C[C@H]1CC[N@@](c2ccccn2)CC1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 7, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 8, 8, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 3, 3, 3, 3, 3, 5, 5, 8, 8, 8, 8, 15, 15, 15, 15, 8, 8, 8, 8, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 61 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464974634 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 Building ZINC000464974634 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000464974634 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 956) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/956: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C[C@H]1CC[N@](c2ccccn2)CC1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000464974634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464974634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000464974634 none CCN(C[C@H]1CC[N@](c2ccccn2)CC1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 7, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 11, 11, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 3, 3, 3, 3, 3, 5, 5, 11, 11, 11, 11, 17, 17, 17, 17, 11, 11, 11, 11, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 68 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 957) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C[C@H]1CC[N@@](c2ccccn2)CC1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000464974634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464974634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000464974634 none CCN(C[C@H]1CC[N@@](c2ccccn2)CC1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 6, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 10, 10, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 5, 9, 9, 3, 3, 2, 2, 2, 2, 2, 4, 4, 10, 10, 10, 10, 16, 16, 16, 16, 10, 10, 10, 10, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3] 50 rigid atoms, others: [2, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 64 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 958) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C[C@H]1CC[N@](c2ccccn2)CC1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000464974634.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000464974634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000464974634 none CCN(C[C@H]1CC[N@](c2ccccn2)CC1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 7, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 9, 9, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 5, 9, 9, 4, 4, 3, 3, 3, 3, 3, 5, 5, 9, 9, 9, 9, 16, 16, 16, 16, 9, 9, 9, 9, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 61 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 959) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C[C@H]1CC[N@@](c2ccccn2)CC1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000464974634.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000464974634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000464974634 none CCN(C[C@H]1CC[N@@](c2ccccn2)CC1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 7, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 8, 8, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 3, 3, 3, 3, 3, 5, 5, 8, 8, 8, 8, 15, 15, 15, 15, 8, 8, 8, 8, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 61 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464974634 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 Building ZINC000464974634 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000464974634 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 956) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/956: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C[C@H]1CC[N@](c2ccccn2)CC1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000464974634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464974634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000464974634 none CCN(C[C@H]1CC[N@](c2ccccn2)CC1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 7, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 11, 11, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 3, 3, 3, 3, 3, 5, 5, 11, 11, 11, 11, 17, 17, 17, 17, 11, 11, 11, 11, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 68 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 957) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C[C@H]1CC[N@@](c2ccccn2)CC1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000464974634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464974634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000464974634 none CCN(C[C@H]1CC[N@@](c2ccccn2)CC1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 6, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 10, 10, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 5, 9, 9, 3, 3, 2, 2, 2, 2, 2, 4, 4, 10, 10, 10, 10, 16, 16, 16, 16, 10, 10, 10, 10, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3] 50 rigid atoms, others: [2, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 64 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 958) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C[C@H]1CC[N@](c2ccccn2)CC1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000464974634.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000464974634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000464974634 none CCN(C[C@H]1CC[N@](c2ccccn2)CC1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 7, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 9, 9, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 5, 9, 9, 4, 4, 3, 3, 3, 3, 3, 5, 5, 9, 9, 9, 9, 16, 16, 16, 16, 9, 9, 9, 9, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 61 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 959) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C[C@H]1CC[N@@](c2ccccn2)CC1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000464974634.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000464974634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000464974634 none CCN(C[C@H]1CC[N@@](c2ccccn2)CC1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 7, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 8, 8, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 3, 3, 3, 3, 3, 5, 5, 8, 8, 8, 8, 15, 15, 15, 15, 8, 8, 8, 8, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 61 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464974634 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464974634 Building ZINC000464976756 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000464976756 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/960 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1) `ZINC000464976756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464976756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976756 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 7, 12, 14, 14, 14, 14, 23, 33, 33, 27, 33, 33, 14, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 14, 14, 14, 14, 23, 23, 33, 33, 33, 33, 33, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/961 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1) `ZINC000464976756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464976756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976756 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 12, 13, 13, 13, 13, 27, 36, 36, 34, 36, 36, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 13, 13, 13, 13, 27, 27, 36, 36, 36, 36, 36, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 150 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/962 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/962' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1) `ZINC000464976756.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000464976756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976756 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 7, 12, 14, 14, 14, 14, 23, 33, 33, 27, 33, 33, 14, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 14, 14, 14, 14, 23, 23, 33, 33, 33, 33, 33, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/963 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/963' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1) `ZINC000464976756.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000464976756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976756 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 12, 13, 13, 13, 13, 27, 36, 36, 34, 36, 36, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 13, 13, 13, 13, 27, 27, 36, 36, 36, 36, 36, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 150 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464976756 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 Building ZINC000464976756 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000464976756 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 960) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/960: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1) `ZINC000464976756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464976756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976756 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 7, 12, 14, 14, 14, 14, 23, 33, 33, 27, 33, 33, 14, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 14, 14, 14, 14, 23, 23, 33, 33, 33, 33, 33, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 961) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/961: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1) `ZINC000464976756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464976756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976756 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 12, 13, 13, 13, 13, 27, 36, 36, 34, 36, 36, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 13, 13, 13, 13, 27, 27, 36, 36, 36, 36, 36, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 150 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 962) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/962: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1) `ZINC000464976756.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000464976756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976756 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 7, 12, 14, 14, 14, 14, 23, 33, 33, 27, 33, 33, 14, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 14, 14, 14, 14, 23, 23, 33, 33, 33, 33, 33, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 963) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1) `ZINC000464976756.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000464976756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976756 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 12, 13, 13, 13, 13, 27, 36, 36, 34, 36, 36, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 13, 13, 13, 13, 27, 27, 36, 36, 36, 36, 36, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 150 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464976756 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 Building ZINC000464976756 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000464976756 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 960) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/960: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1) `ZINC000464976756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464976756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976756 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 7, 12, 14, 14, 14, 14, 23, 33, 33, 27, 33, 33, 14, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 14, 14, 14, 14, 23, 23, 33, 33, 33, 33, 33, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 961) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/961: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1) `ZINC000464976756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464976756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976756 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 12, 13, 13, 13, 13, 27, 36, 36, 34, 36, 36, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 13, 13, 13, 13, 27, 27, 36, 36, 36, 36, 36, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 150 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 962) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/962: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1) `ZINC000464976756.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000464976756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976756 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 7, 12, 14, 14, 14, 14, 23, 33, 33, 27, 33, 33, 14, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 14, 14, 14, 14, 23, 23, 33, 33, 33, 33, 33, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 963) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1) `ZINC000464976756.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000464976756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976756 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 12, 13, 13, 13, 13, 27, 36, 36, 34, 36, 36, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 13, 13, 13, 13, 27, 27, 36, 36, 36, 36, 36, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 150 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464976756 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 Building ZINC000464976756 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000464976756 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 960) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/960: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1) `ZINC000464976756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464976756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976756 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 7, 12, 14, 14, 14, 14, 23, 33, 33, 27, 33, 33, 14, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 14, 14, 14, 14, 23, 23, 33, 33, 33, 33, 33, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 961) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/961: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1) `ZINC000464976756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464976756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976756 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 12, 13, 13, 13, 13, 27, 36, 36, 34, 36, 36, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 13, 13, 13, 13, 27, 27, 36, 36, 36, 36, 36, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 150 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 962) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/962: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1) `ZINC000464976756.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000464976756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976756 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 7, 12, 14, 14, 14, 14, 23, 33, 33, 27, 33, 33, 14, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 14, 14, 14, 14, 23, 23, 33, 33, 33, 33, 33, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 963) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1) `ZINC000464976756.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000464976756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976756 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 12, 13, 13, 13, 13, 27, 36, 36, 34, 36, 36, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 13, 13, 13, 13, 27, 27, 36, 36, 36, 36, 36, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 150 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464976756 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976756 Building ZINC000464976757 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000464976757 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/964 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1) `ZINC000464976757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464976757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976757 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 12, 13, 13, 13, 13, 28, 38, 38, 28, 38, 38, 13, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 13, 13, 13, 13, 28, 28, 38, 38, 28, 38, 38, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/965 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1) `ZINC000464976757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464976757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976757 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 7, 12, 13, 13, 13, 13, 22, 33, 33, 26, 33, 33, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 13, 13, 13, 13, 22, 22, 33, 33, 24, 33, 33, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/966 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/966' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1) `ZINC000464976757.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000464976757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976757 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 12, 13, 13, 13, 13, 28, 38, 38, 28, 38, 38, 13, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 13, 13, 13, 13, 28, 28, 38, 38, 28, 38, 38, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/967 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/967' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1) `ZINC000464976757.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000464976757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976757 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 7, 12, 13, 13, 13, 13, 22, 33, 33, 26, 33, 33, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 13, 13, 13, 13, 22, 22, 33, 33, 24, 33, 33, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464976757 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 Building ZINC000464976757 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000464976757 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 964) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/964: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1) `ZINC000464976757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464976757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976757 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 12, 13, 13, 13, 13, 28, 38, 38, 28, 38, 38, 13, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 13, 13, 13, 13, 28, 28, 38, 38, 28, 38, 38, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 965) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/965: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1) `ZINC000464976757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464976757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976757 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 7, 12, 13, 13, 13, 13, 22, 33, 33, 26, 33, 33, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 13, 13, 13, 13, 22, 22, 33, 33, 24, 33, 33, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 966) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/966: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1) `ZINC000464976757.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000464976757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976757 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 12, 13, 13, 13, 13, 28, 38, 38, 28, 38, 38, 13, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 13, 13, 13, 13, 28, 28, 38, 38, 28, 38, 38, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 967) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/967: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1) `ZINC000464976757.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000464976757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976757 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 7, 12, 13, 13, 13, 13, 22, 33, 33, 26, 33, 33, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 13, 13, 13, 13, 22, 22, 33, 33, 24, 33, 33, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464976757 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 Building ZINC000464976757 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000464976757 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 964) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/964: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1) `ZINC000464976757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464976757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976757 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 12, 13, 13, 13, 13, 28, 38, 38, 28, 38, 38, 13, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 13, 13, 13, 13, 28, 28, 38, 38, 28, 38, 38, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 965) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/965: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1) `ZINC000464976757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464976757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976757 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 7, 12, 13, 13, 13, 13, 22, 33, 33, 26, 33, 33, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 13, 13, 13, 13, 22, 22, 33, 33, 24, 33, 33, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 966) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/966: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1) `ZINC000464976757.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000464976757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976757 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 12, 13, 13, 13, 13, 28, 38, 38, 28, 38, 38, 13, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 13, 13, 13, 13, 28, 28, 38, 38, 28, 38, 38, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 967) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/967: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1) `ZINC000464976757.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000464976757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976757 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 7, 12, 13, 13, 13, 13, 22, 33, 33, 26, 33, 33, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 13, 13, 13, 13, 22, 22, 33, 33, 24, 33, 33, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464976757 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 Building ZINC000464976757 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000464976757 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 964) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/964: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1) `ZINC000464976757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464976757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976757 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 12, 13, 13, 13, 13, 28, 38, 38, 28, 38, 38, 13, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 13, 13, 13, 13, 28, 28, 38, 38, 28, 38, 38, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 965) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/965: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1) `ZINC000464976757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464976757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976757 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 7, 12, 13, 13, 13, 13, 22, 33, 33, 26, 33, 33, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 13, 13, 13, 13, 22, 22, 33, 33, 24, 33, 33, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `2' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/2 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 2 (index: 966) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/966: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1) `ZINC000464976757.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000464976757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976757 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 12, 13, 13, 13, 13, 28, 38, 38, 28, 38, 38, 13, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 13, 13, 13, 13, 28, 28, 38, 38, 28, 38, 38, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `3' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/3 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 3 (index: 967) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/967: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1) `ZINC000464976757.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000464976757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000464976757 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 7, 12, 13, 13, 13, 13, 22, 33, 33, 26, 33, 33, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 13, 13, 13, 13, 22, 22, 33, 33, 24, 33, 33, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000464976757 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 3: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/3.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/1.* 2: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757/2.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000464976757 Building ZINC000542068771 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542068771 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/968 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000542068771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542068771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000542068771 none O=C(N1CCO[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 10, 10, 10, 10, 10, 10, 25, 25, 10, 14, 25, 25, 25, 25, 25, 10, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 25, 25, 25, 25, 10, 10, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/969 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000542068771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542068771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000542068771 none O=C(N1CCO[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 7, 12, 12, 12, 12, 12, 12, 29, 29, 12, 29, 29, 29, 29, 29, 29, 12, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 12, 12, 12, 12, 29, 29, 29, 29, 12, 12, 6, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000542068771 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771 Building ZINC000542068771 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542068771 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 968) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/968: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000542068771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542068771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000542068771 none O=C(N1CCO[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 10, 10, 10, 10, 10, 10, 25, 25, 10, 14, 25, 25, 25, 25, 25, 10, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 25, 25, 25, 25, 10, 10, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 969) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/969: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000542068771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542068771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000542068771 none O=C(N1CCO[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 7, 12, 12, 12, 12, 12, 12, 29, 29, 12, 29, 29, 29, 29, 29, 29, 12, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 12, 12, 12, 12, 29, 29, 29, 29, 12, 12, 6, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000542068771 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068771 Building ZINC000542068772 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542068772 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/970 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000542068772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542068772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000542068772 none O=C(N1CCO[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 10, 10, 10, 10, 10, 10, 29, 29, 10, 10, 29, 29, 29, 29, 29, 10, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 10, 10, 10, 10, 29, 29, 29, 29, 10, 10, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/971 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000542068772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542068772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000542068772 none O=C(N1CCO[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 10, 10, 10, 10, 10, 10, 26, 26, 10, 10, 26, 26, 26, 26, 26, 10, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000542068772 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772 Building ZINC000542068772 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542068772 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 970) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/970: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000542068772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542068772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000542068772 none O=C(N1CCO[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 10, 10, 10, 10, 10, 10, 29, 29, 10, 10, 29, 29, 29, 29, 29, 10, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 10, 10, 10, 10, 29, 29, 29, 29, 10, 10, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 971) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/971: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000542068772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542068772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000542068772 none O=C(N1CCO[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 10, 10, 10, 10, 10, 10, 26, 26, 10, 10, 26, 26, 26, 26, 26, 10, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000542068772 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542068772 Building ZINC000465004376 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465004376 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/972 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1OC(F)F) `ZINC000465004376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465004376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000465004376 none CCOc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 17, 17, 17, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 17, 17, 28, 35, 35, 46, 46, 46, 46, 46, 17, 17, 17, 7, 7, 1, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 35] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/973 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cccc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1OC(F)F) `ZINC000465004376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465004376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000465004376 none CCOc1cccc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 44, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 16, 16, 27, 34, 34, 45, 45, 45, 45, 45, 16, 16, 16, 6, 6, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 34] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000465004376 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376 Building ZINC000465004376 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465004376 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 972) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/972: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1OC(F)F) `ZINC000465004376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465004376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000465004376 none CCOc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 17, 17, 17, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 17, 17, 28, 35, 35, 46, 46, 46, 46, 46, 17, 17, 17, 7, 7, 1, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 35] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 973) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cccc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1OC(F)F) `ZINC000465004376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465004376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000465004376 none CCOc1cccc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 44, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 16, 16, 27, 34, 34, 45, 45, 45, 45, 45, 16, 16, 16, 6, 6, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 34] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000465004376 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465004376 Building ZINC000303060729 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303060729 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/974 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CN2CCSCC2)c1) `ZINC000303060729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303060729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000303060729 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CN2CCSCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 14, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 3, 10, 10, 37, 37, 37, 37, 37, 37, 10, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 10, 10, 9, 34, 34, 37, 37, 37, 37, 37, 37, 37, 37, 10] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 160 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/975 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CN2CCSCC2)c1) `ZINC000303060729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303060729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000303060729 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CN2CCSCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 14, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 9, 10, 10, 40, 40, 40, 40, 40, 40, 10, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 10, 10, 10, 36, 36, 40, 40, 40, 40, 40, 40, 40, 40, 10] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000303060729 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729 Building ZINC000303060729 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303060729 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 974) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/974: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CN2CCSCC2)c1) `ZINC000303060729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303060729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000303060729 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CN2CCSCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 14, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 3, 10, 10, 37, 37, 37, 37, 37, 37, 10, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 10, 10, 9, 34, 34, 37, 37, 37, 37, 37, 37, 37, 37, 10] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 160 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 975) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/975: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CN2CCSCC2)c1) `ZINC000303060729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303060729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000303060729 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CN2CCSCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 14, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 9, 10, 10, 40, 40, 40, 40, 40, 40, 10, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 10, 10, 10, 36, 36, 40, 40, 40, 40, 40, 40, 40, 40, 10] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000303060729 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303060729 Building ZINC000465017119 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465017119 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/976 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC(F)F)c(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000465017119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465017119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000465017119 none COc1ccc(OC(F)F)c(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 21, 21, 21, 21, 21, 34, 34, 34, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 21, 25, 25, 25, 21, 21, 34, 8, 8, 2, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 21] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/977 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC(F)F)c(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000465017119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465017119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000465017119 none COc1ccc(OC(F)F)c(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 21, 21, 21, 21, 21, 35, 35, 35, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 21, 25, 25, 25, 21, 21, 35, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 21] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000465017119 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119 Building ZINC000465017119 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465017119 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 976) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/976: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC(F)F)c(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000465017119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465017119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000465017119 none COc1ccc(OC(F)F)c(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 21, 21, 21, 21, 21, 34, 34, 34, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 21, 25, 25, 25, 21, 21, 34, 8, 8, 2, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 21] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 977) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/977: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC(F)F)c(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000465017119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465017119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000465017119 none COc1ccc(OC(F)F)c(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 21, 21, 21, 21, 21, 35, 35, 35, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 21, 25, 25, 25, 21, 21, 35, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 21] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000465017119 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465017119 Building ZINC000465085857 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465085857 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/978 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cc(N(C)C)nc2ccccc12) `ZINC000465085857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465085857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000465085857 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cc(N(C)C)nc2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 15, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 102 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/979 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cc(N(C)C)nc2ccccc12) `ZINC000465085857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465085857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000465085857 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cc(N(C)C)nc2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 15, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 7, 7, 4, 7, 7, 3, 3, 3, 3, 15, 15, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 109 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000465085857 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857 Building ZINC000465085857 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465085857 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 978) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/978: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cc(N(C)C)nc2ccccc12) `ZINC000465085857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465085857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000465085857 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cc(N(C)C)nc2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 15, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 102 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 979) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/979: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cc(N(C)C)nc2ccccc12) `ZINC000465085857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465085857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000465085857 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cc(N(C)C)nc2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 15, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 7, 7, 4, 7, 7, 3, 3, 3, 3, 15, 15, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 109 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000465085857 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465085857 Building ZINC000542202218 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542202218 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/980 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCc1nc(c2ccc(F)cc2)no1) `ZINC000542202218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542202218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000542202218 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCc1nc(c2ccc(F)cc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 9, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 10, 10, 12, 12, 12, 14, 50, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/981 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCc1nc(c2ccc(F)cc2)no1) `ZINC000542202218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542202218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000542202218 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCc1nc(c2ccc(F)cc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 8, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 9, 9, 10, 9, 50, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000542202218 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218 Building ZINC000542202218 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542202218 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 980) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/980: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCc1nc(c2ccc(F)cc2)no1) `ZINC000542202218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542202218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000542202218 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCc1nc(c2ccc(F)cc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 9, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 10, 10, 12, 12, 12, 14, 50, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 981) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/981: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCc1nc(c2ccc(F)cc2)no1) `ZINC000542202218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542202218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000542202218 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCc1nc(c2ccc(F)cc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 8, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 9, 9, 10, 9, 50, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000542202218 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000542202218 Building ZINC000465332032 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465332032 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/982 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)nc3cc(Br)ccc32)cc1) `ZINC000465332032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465332032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000465332032 none Cc1ccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)nc3cc(Br)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 18, 32, 32, 18, 18, 7, 7, 1, 7, 1, 1, 1, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 32, 32, 32, 32, 32, 32, 32, 7, 12, 12, 12, 12, 12, 18, 18, 18, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/983 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(n2c(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)nc3cc(Br)ccc32)cc1) `ZINC000465332032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465332032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000465332032 none Cc1ccc(n2c(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)nc3cc(Br)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 29, 29, 17, 17, 6, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 29, 29, 29, 29, 29, 29, 29, 6, 11, 11, 11, 11, 11, 17, 17, 17, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 81 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000465332032 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032 Building ZINC000465332032 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465332032 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 982) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/982: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)nc3cc(Br)ccc32)cc1) `ZINC000465332032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465332032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000465332032 none Cc1ccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)nc3cc(Br)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 18, 32, 32, 18, 18, 7, 7, 1, 7, 1, 1, 1, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 32, 32, 32, 32, 32, 32, 32, 7, 12, 12, 12, 12, 12, 18, 18, 18, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 983) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/983: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(n2c(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)nc3cc(Br)ccc32)cc1) `ZINC000465332032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465332032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000465332032 none Cc1ccc(n2c(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)nc3cc(Br)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 29, 29, 17, 17, 6, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 29, 29, 29, 29, 29, 29, 29, 6, 11, 11, 11, 11, 11, 17, 17, 17, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 81 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000465332032 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465332032 Building ZINC000465356727 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465356727 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/984 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1Oc2cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O) `ZINC000465356727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465356727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000465356727 none CC[C@H]1Oc2cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 23, 23, 23, 23, 23, 15, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 22, 23, 23, 23, 23, 23, 31, 31, 31, 31, 31, 23, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 23, 23, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 115 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/985 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1Oc2cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O) `ZINC000465356727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465356727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000465356727 none CC[C@H]1Oc2cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 19, 19, 19, 19, 13, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 19, 19, 19, 19, 19, 19, 27, 27, 27, 27, 27, 19, 4, 4, 4, 2, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 19, 19, 19] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000465356727 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727 Building ZINC000465356727 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465356727 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 984) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/984: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1Oc2cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O) `ZINC000465356727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465356727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000465356727 none CC[C@H]1Oc2cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 23, 23, 23, 23, 23, 15, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 22, 23, 23, 23, 23, 23, 31, 31, 31, 31, 31, 23, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 23, 23, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 115 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 985) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/985: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1Oc2cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O) `ZINC000465356727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465356727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000465356727 none CC[C@H]1Oc2cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 19, 19, 19, 19, 13, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 19, 19, 19, 19, 19, 19, 27, 27, 27, 27, 27, 19, 4, 4, 4, 2, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 19, 19, 19] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000465356727 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356727 Building ZINC000465356728 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465356728 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/986 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1Oc2cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O) `ZINC000465356728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465356728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000465356728 none CC[C@H]1Oc2cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 21, 21, 21, 21, 21, 14, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 21, 21, 21, 21, 21, 21, 32, 32, 32, 32, 32, 21, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 21, 21, 21] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 131 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/987 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1Oc2cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O) `ZINC000465356728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465356728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000465356728 none CC[C@H]1Oc2cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 21, 21, 21, 21, 21, 15, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 21, 21, 21, 21, 21, 21, 28, 28, 28, 28, 28, 21, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 21, 21, 21] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 98 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000465356728 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728 Building ZINC000465356728 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465356728 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 986) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/986: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1Oc2cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O) `ZINC000465356728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465356728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000465356728 none CC[C@H]1Oc2cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 21, 21, 21, 21, 21, 14, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 21, 21, 21, 21, 21, 21, 32, 32, 32, 32, 32, 21, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 21, 21, 21] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 131 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 987) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/987: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1Oc2cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O) `ZINC000465356728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465356728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000465356728 none CC[C@H]1Oc2cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 21, 21, 21, 21, 21, 15, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 21, 21, 21, 21, 21, 21, 28, 28, 28, 28, 28, 21, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 21, 21, 21] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 98 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000465356728 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356728 Building ZINC000465356729 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465356729 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/988 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1Oc2cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O) `ZINC000465356729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465356729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000465356729 none CC[C@@H]1Oc2cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 24, 24, 24, 24, 16, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 21, 24, 24, 24, 24, 24, 31, 31, 31, 31, 31, 24, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 122 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/989 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1Oc2cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O) `ZINC000465356729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465356729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000465356729 none CC[C@@H]1Oc2cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 21, 21, 21, 21, 21, 14, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 20, 21, 21, 21, 21, 21, 32, 32, 32, 32, 32, 21, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 21, 21, 21] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 128 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000465356729 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729 Building ZINC000465356729 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465356729 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 988) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/988: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1Oc2cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O) `ZINC000465356729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465356729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000465356729 none CC[C@@H]1Oc2cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 24, 24, 24, 24, 16, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 21, 24, 24, 24, 24, 24, 31, 31, 31, 31, 31, 24, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 122 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 989) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/989: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1Oc2cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O) `ZINC000465356729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465356729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000465356729 none CC[C@@H]1Oc2cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 21, 21, 21, 21, 21, 14, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 20, 21, 21, 21, 21, 21, 32, 32, 32, 32, 32, 21, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 21, 21, 21] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 128 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000465356729 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356729 Building ZINC000465356730 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465356730 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/990 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1Oc2cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O) `ZINC000465356730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465356730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000465356730 none CC[C@@H]1Oc2cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 22, 22, 22, 22, 22, 14, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 19, 22, 22, 22, 22, 22, 30, 30, 30, 30, 30, 22, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 22, 22, 22] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 126 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/991 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/991' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1Oc2cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O) `ZINC000465356730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465356730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000465356730 none CC[C@@H]1Oc2cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 19, 19, 19, 19, 12, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 18, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 19, 4, 4, 4, 2, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 19, 19, 19] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 114 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000465356730 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730 Building ZINC000465356730 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465356730 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 990) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1Oc2cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O) `ZINC000465356730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465356730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000465356730 none CC[C@@H]1Oc2cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 22, 22, 22, 22, 22, 14, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 19, 22, 22, 22, 22, 22, 30, 30, 30, 30, 30, 22, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 22, 22, 22] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 126 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 991) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1Oc2cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O) `ZINC000465356730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465356730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000465356730 none CC[C@@H]1Oc2cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 19, 19, 19, 19, 12, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 18, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 19, 4, 4, 4, 2, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 19, 19, 19] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 114 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000465356730 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000465356730 Building ZINC000303428260 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303428260 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/992 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CS(=O)(=O)C(C)C)c1) `ZINC000303428260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303428260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000303428260 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CS(=O)(=O)C(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 11, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 5, 5, 5, 13, 13, 5, 13, 13, 23, 34, 34, 34, 36, 36, 13, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 5, 13, 13, 5, 23, 23, 36, 36, 36, 36, 36, 36, 36, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 190 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/993 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/993' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CS(=O)(=O)C(C)C)c1) `ZINC000303428260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303428260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000303428260 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CS(=O)(=O)C(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 11, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 26, 37, 37, 37, 38, 38, 13, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 5, 13, 13, 13, 26, 26, 38, 38, 38, 38, 38, 38, 38, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 176 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000303428260 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260 Building ZINC000303428260 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303428260 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 992) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/992: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CS(=O)(=O)C(C)C)c1) `ZINC000303428260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303428260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000303428260 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CS(=O)(=O)C(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 11, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 5, 5, 5, 13, 13, 5, 13, 13, 23, 34, 34, 34, 36, 36, 13, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 5, 13, 13, 5, 23, 23, 36, 36, 36, 36, 36, 36, 36, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 190 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 993) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/993: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CS(=O)(=O)C(C)C)c1) `ZINC000303428260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303428260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000303428260 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CS(=O)(=O)C(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 11, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 26, 37, 37, 37, 38, 38, 13, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 5, 13, 13, 13, 26, 26, 38, 38, 38, 38, 38, 38, 38, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 176 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000303428260 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000303428260 Building ZINC000491495518 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000491495518 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/994 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(S(=O)(=O)C2CCCCC2)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000491495518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000491495518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000491495518 none O=C(Nc1cccc(S(=O)(=O)C2CCCCC2)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 2, 9, 9, 14, 14, 15, 31, 31, 31, 31, 31, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 9, 9, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 9, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/995 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(S(=O)(=O)C2CCCCC2)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000491495518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000491495518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000491495518 none O=C(Nc1cccc(S(=O)(=O)C2CCCCC2)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 10, 2, 10, 10, 15, 15, 16, 30, 30, 30, 30, 30, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 10, 10, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000491495518 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518 Building ZINC000491495518 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000491495518 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 994) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/994: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(S(=O)(=O)C2CCCCC2)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000491495518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000491495518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000491495518 none O=C(Nc1cccc(S(=O)(=O)C2CCCCC2)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 2, 9, 9, 14, 14, 15, 31, 31, 31, 31, 31, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 9, 9, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 9, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 995) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/995: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(S(=O)(=O)C2CCCCC2)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000491495518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000491495518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000491495518 none O=C(Nc1cccc(S(=O)(=O)C2CCCCC2)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 10, 2, 10, 10, 15, 15, 16, 30, 30, 30, 30, 30, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 10, 10, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000491495518 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491495518 Building ZINC000491529203 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000491529203 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/996 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCNc1cccc(Br)c1) `ZINC000491529203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000491529203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000491529203 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCNc1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 17, 24, 50, 50, 44, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 11, 11, 17, 17, 24, 50, 50, 44, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/997 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCNc1cccc(Br)c1) `ZINC000491529203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000491529203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000491529203 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCNc1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 17, 24, 50, 50, 43, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 11, 11, 17, 17, 24, 50, 50, 43, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000491529203 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203 Building ZINC000491529203 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000491529203 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 996) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/996: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCNc1cccc(Br)c1) `ZINC000491529203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000491529203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000491529203 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCNc1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 17, 24, 50, 50, 44, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 11, 11, 17, 17, 24, 50, 50, 44, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 997) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/997: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCNc1cccc(Br)c1) `ZINC000491529203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000491529203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000491529203 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCNc1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 17, 24, 50, 50, 43, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 11, 11, 17, 17, 24, 50, 50, 43, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000491529203 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000491529203 Building ZINC000669953290 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000669953290 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/998 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)s2)cs1) `ZINC000669953290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000669953290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000669953290 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)s2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 17, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 42, 42, 42, 42, 42, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 42, 42, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/999 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/999' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)s2)cs1) `ZINC000669953290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000669953290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000669953290 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)s2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 17, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 42, 42, 42, 42, 42, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 42, 42, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000669953290 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290 Building ZINC000669953290 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000669953290 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 998) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/998: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)s2)cs1) `ZINC000669953290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000669953290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000669953290 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)s2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 17, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 42, 42, 42, 42, 42, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 42, 42, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 mkdir: created directory `1' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290/1 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 1 (index: 999) grep: /scratch/xiaobo/216447/xad-8058088.4/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)s2)cs1) `ZINC000669953290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000669953290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000669953290 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)s2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 17, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 42, 42, 42, 42, 42, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 42, 42, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000669953290 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290/0.* 1: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290/1.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000669953290 Building ZINC000493150358 mkdir: created directory `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000493150358' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000493150358 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC000493150358 mkdir: created directory `0' /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000493150358/0 /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000493150358 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/216447/xad-8058088.4/working/3D/1000 `/scratch/xiaobo/216447/xad-8058088.4/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000493150358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000493150358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000493150358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000493150358 none COC(=O)CCCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 15, 37, 6, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 37, 37, 37, 14, 14, 7, 7, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2] 50 rigid atoms, others: [6, 7, 8, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000493150358 /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Finished preparing ZINC000493150358 Recording results /scratch/xiaobo/216447/xad-8058088.4/working /scratch/xiaobo/216447/xad-8058088.4 Appending to /scratch/xiaobo/216447/xad-8058088.4/finished/xad.* 0: /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000493150358/0.* Removing working files in /scratch/xiaobo/216447/xad-8058088.4/working/building/ZINC000493150358 /scratch/xiaobo/216447/xad-8058088.4 Compressing combined databse files /scratch/xiaobo/216447/xad-8058088.4/finished/xad.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/216447/xad-8058088.4/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/216447/xad-8058088.4/working/3D/1001' removed directory: `/scratch/xiaobo/216447/xad-8058088.4/working/3D' rmdir: removing directory, `/scratch/xiaobo/216447/xad-8058088.4/working/building' rmdir: removing directory, `/scratch/xiaobo/216447/xad-8058088.4/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs `/scratch/xiaobo/216447/xad-8058088.4' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xad' `/scratch/xiaobo/216447/xad-8058088.4/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xad/finished' `/scratch/xiaobo/216447/xad-8058088.4/finished/xad.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xad/finished/xad.db2.gz' removed `/scratch/xiaobo/216447/xad-8058088.4/finished/xad.db2.gz' removed directory: `/scratch/xiaobo/216447/xad-8058088.4/finished' removed directory: `/scratch/xiaobo/216447/xad-8058088.4'